dbSNP rs17099207: ENSG00000258964:n.149-4481G>A (chr14-61762395-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 ENST00000555937.1(ENSG00000258964):n.149-4481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,563,608 control chromosomes in the GnomAD database, including 66,687 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 0.32 ( 7976 hom., cov: 32)

Exomes 𝑓: 0.28 ( 58711 hom. )

Consequence

ENSG00000258964
ENST00000555937.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340

Publications

10 publications found

Variant links:

Genes affected

ENSG00000258964 (HGNC:):

ENSG00000258964 links:

SNAPC1 (HGNC:11134): (small nuclear RNA activating complex polypeptide 1) Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SNAPC1 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=-0.75).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNAPC1	NM_003082.4 link	c.-66G>A		upstream_gene_variant		ENST00000216294.5	NP_003073.1	Q16533B2RC42

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258964	ENST00000555937.1 link	n.149-4481G>A		intron_variant	Intron 1 of 4	4
SNAPC1	ENST00000216294.5 link	c.-66G>A		upstream_gene_variant		1	NM_003082.4	ENSP00000216294.4		Q16533

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48059

AN:

151168

Hom.:

7942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.314

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.340

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.331

GnomAD4 exome

AF:

0.284

AC:

401103

AN:

1412320

Hom.:

58711

Cov.:

AF XY:

0.286

AC XY:

200920

AN XY:

701722

show subpopulations

African (AFR)

AF:

0.380

AC:

12170

AN:

32068

American (AMR)

AF:

0.367

AC:

13702

AN:

37332

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

6727

AN:

25174

East Asian (EAS)

AF:

0.206

AC:

7656

AN:

37112

South Asian (SAS)

AF:

0.382

AC:

31500

AN:

82364

European-Finnish (FIN)

AF:

0.271

AC:

10727

AN:

39624

Middle Eastern (MID)

AF:

0.319

AC:

1330

AN:

4164

European-Non Finnish (NFE)

AF:

0.273

AC:

299708

AN:

1095904

Other (OTH)

AF:

0.300

AC:

17583

AN:

58578

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

12589

25177

37766

50354

62943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.318

AC:

48136

AN:

151288

Hom.:

7976

Cov.:

AF XY:

0.320

AC XY:

23678

AN XY:

73894

show subpopulations

African (AFR)

AF:

0.382

AC:

15750

AN:

41256

American (AMR)

AF:

0.368

AC:

5612

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

952

AN:

3464

East Asian (EAS)

AF:

0.231

AC:

1148

AN:

4974

South Asian (SAS)

AF:

0.390

AC:

1856

AN:

4756

European-Finnish (FIN)

AF:

0.262

AC:

2761

AN:

10544

Middle Eastern (MID)

AF:

0.349

AC:

102

AN:

292

European-Non Finnish (NFE)

AF:

0.280

AC:

18981

AN:

67764

Other (OTH)

AF:

0.330

AC:

692

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

1463

2926

4388

5851

7314

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.306

Hom.:

919

Bravo

AF:

0.327

Asia WGS

AF:

0.344

AC:

1197

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

6.9

(source)

DANN

Benign

0.87

PhyloP100

0.034

PromoterAI

0.60

Over-expression

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

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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rs17099207

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over