rs10510985

Variant names:

• chr3-69614720-C-T
• rs10510985

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 0.43 in 151,894 control chromosomes in the GnomAD database, including 15,599 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 0.43 (15599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.431 AC: 65342 AN: 151776 Hom.: 15590 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.430 AC: 65374 AN: 151894 Hom.: 15599 Cov.: 31 AF XY: 0.433 AC XY: 32150 AN XY: 74250

African (AFR) AF: 0.256 AC: 10602 AN: 41412

American (AMR) AF: 0.560 AC: 8551 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4343 AN: 5160

South Asian (SAS) AF: 0.550 AC: 2649 AN: 4812

European-Finnish (FIN) AF: 0.392 AC: 4131 AN: 10538

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31960 AN: 67926

Other (OTH) AF: 0.428 AC: 903 AN: 2112

Alfa AF: 0.464 Hom.: 28794

Bravo AF: 0.436

Asia WGS AF: 0.618 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10510985; hg19: chr3-69663871;