rs964681

Variant names:

• chr10-130900156-T-C
• rs964681

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 0.375 in 152,174 control chromosomes in the GnomAD database, including 10,989 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 0.37 (10989 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 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: 0.375 AC: 56989 AN: 152056 Hom.: 10984 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.375 AC: 57017 AN: 152174 Hom.: 10989 Cov.: 33 AF XY: 0.377 AC XY: 28044 AN XY: 74404

African (AFR) AF: 0.287 AC: 11913 AN: 41504

American (AMR) AF: 0.373 AC: 5705 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5176

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4824

European-Finnish (FIN) AF: 0.429 AC: 4546 AN: 10600

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28401 AN: 67990

Other (OTH) AF: 0.392 AC: 828 AN: 2114

Alfa AF: 0.400 Hom.: 46201

Bravo AF: 0.363

Asia WGS AF: 0.356 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs964681; hg19: chr10-132698419; COSMIC: COSV54092843;