dbSNP rs7758616: ENSG00000285639:n.106+11165C>T (chr6-14199916-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000650535.1(ENSG00000285639):n.106+11165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,084 control chromosomes in the GnomAD database, including 2,048 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.091 ( 2048 hom., cov: 32)

Consequence

ENSG00000285639
ENST00000650535.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347

Publications

4 publications found

Variant links:

Genes affected

ENSG00000285639 (HGNC:):

ENSG00000285639 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374940	XR_926501.2 link	n.1665+714C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285639	ENST00000650535.1 link	n.106+11165C>T	intron_variant	Intron 1 of 1
ENSG00000285639	ENST00000724691.1 link	n.139-4640C>T	intron_variant	Intron 1 of 1
ENSG00000285639	ENST00000724692.1 link	n.119+714C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0902

AC:

13712

AN:

151966

Hom.:

2033

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0319

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00179

Gnomad OTH

AF:

0.0683

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0905

AC:

13771

AN:

152084

Hom.:

2048

Cov.:

AF XY:

0.0872

AC XY:

6484

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.310

AC:

12823

AN:

41396

American (AMR)

AF:

0.0319

AC:

488

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0490

AC:

170

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.00311

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.000283

AC:

AN:

10592

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00179

AC:

122

AN:

68022

Other (OTH)

AF:

0.0676

AC:

143

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

486

972

1458

1944

2430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0828

Hom.:

1372

Bravo

AF:

0.103

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.63

(source)

DANN

Benign

0.68

PhyloP100

-0.35

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over