rs9602785

Variant names:

• chr13-85634269-T-C
• rs9602785
• ENST00000761619.1:n.171-2427A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761619.1(ENSG00000299208):​n.171-2427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,070 control chromosomes in the GnomAD database, including 1,643 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 0.14 (1643 hom., cov: 32)
• Consequence: ENSG00000299208 ENST00000761619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 1 publications found

Genes affected

ENSG00000299208 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299208	ENST00000761619.1	n.171-2427A>G		intron_variant	Intron 1 of 2
ENSG00000299208	ENST00000761620.1	n.169-2427A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21170 AN: 151952 Hom.: 1631 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0936

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.140 AC: 21216 AN: 152070 Hom.: 1643 Cov.: 32 AF XY: 0.137 AC XY: 10186 AN XY: 74340

African (AFR) AF: 0.185 AC: 7669 AN: 41502

American (AMR) AF: 0.0936 AC: 1427 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3464

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5172

South Asian (SAS) AF: 0.0519 AC: 250 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1734 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9579 AN: 67954

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.145 Hom.: 282

Bravo AF: 0.134

Asia WGS AF: 0.0440 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs9602785; hg19: chr13-86208404;