rs10949808

Variant names:

• chr7-156255955-T-G
• rs10949808

Variant summary

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

The variant allele was found at a frequency of 0.453 in 152,078 control chromosomes in the GnomAD database, including 17,808 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 0.45 (17808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 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

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68897 AN: 151960 Hom.: 17794 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.453 AC: 68949 AN: 152078 Hom.: 17808 Cov.: 32 AF XY: 0.449 AC XY: 33421 AN XY: 74352

African (AFR) AF: 0.227 AC: 9403 AN: 41496

American (AMR) AF: 0.472 AC: 7204 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3466

East Asian (EAS) AF: 0.0956 AC: 495 AN: 5178

South Asian (SAS) AF: 0.466 AC: 2243 AN: 4814

European-Finnish (FIN) AF: 0.556 AC: 5877 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40474 AN: 67968

Other (OTH) AF: 0.474 AC: 1001 AN: 2110

Alfa AF: 0.547 Hom.: 38252

Bravo AF: 0.434

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.66
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10949808; hg19: chr7-156048649;