dbSNP rs6976789: SCRN1:c.*639G>A (chr7-29923318-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014766.5(SCRN1):c.*639G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,164 control chromosomes in the GnomAD database, including 9,353 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 9340 hom., cov: 32)

Exomes 𝑓: 0.39 ( 13 hom. )

Consequence

SCRN1
NM_014766.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.20

Publications

15 publications found

Variant links:

Genes affected

SCRN1 (HGNC:22192): (secernin 1) This gene likely encodes a member of the secernin family of proteins. A similar protein in rat functions in regulation of exocytosis in mast cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

SCRN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 7-29923318-C-T is Benign according to our data. Variant chr7-29923318-C-T is described in ClinVar as Benign. ClinVar VariationId is 1257931.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014766.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SCRN1	NM_014766.5	MANE Select	c.*639G>A	3_prime_UTR	Exon 8 of 8	NP_055581.3
SCRN1	NM_001145514.1		c.*639G>A	3_prime_UTR	Exon 8 of 8	NP_001138986.1
SCRN1	NM_001145513.1		c.*639G>A	3_prime_UTR	Exon 8 of 8	NP_001138985.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SCRN1	ENST00000242059.10	TSL:1 MANE Select	c.*639G>A	3_prime_UTR	Exon 8 of 8	ENSP00000242059.5
SCRN1	ENST00000426154.5	TSL:5	c.*639G>A	3_prime_UTR	Exon 8 of 8	ENSP00000409068.1
SCRN1	ENST00000425819.6	TSL:2	c.*639G>A	downstream_gene	N/A	ENSP00000414245.2

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52542

AN:

151912

Hom.:

9320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.407

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.355

GnomAD4 exome

AF:

0.386

AC:

AN:

132

Hom.:

Cov.:

AF XY:

0.466

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.402

AC:

AN:

Other (OTH)

AF:

0.286

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.346

AC:

52593

AN:

152032

Hom.:

9340

Cov.:

AF XY:

0.345

AC XY:

25642

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.407

AC:

16879

AN:

41448

American (AMR)

AF:

0.281

AC:

4291

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.381

AC:

1321

AN:

3470

East Asian (EAS)

AF:

0.182

AC:

942

AN:

5170

South Asian (SAS)

AF:

0.303

AC:

1455

AN:

4808

European-Finnish (FIN)

AF:

0.380

AC:

4009

AN:

10554

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.331

AC:

22525

AN:

67988

Other (OTH)

AF:

0.352

AC:

743

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1772

3544

5315

7087

8859

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.335

Hom.:

15040

Bravo

AF:

0.340

Asia WGS

AF:

0.268

AC:

934

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 15, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 25399950)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.018

(source)

DANN

Benign

0.32

PhyloP100

-3.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over