rs3862556

Variant names:

• chr10-74781229-C-T
• rs3862556

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 0.0579 in 152,084 control chromosomes in the GnomAD database, including 480 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 0.058 (480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 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: 0.0579 AC: 8803 AN: 151966 Hom.: 478 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0579 AC: 8803 AN: 152084 Hom.: 480 Cov.: 32 AF XY: 0.0606 AC XY: 4505 AN XY: 74326

African (AFR) AF: 0.0167 AC: 693 AN: 41504

American (AMR) AF: 0.104 AC: 1582 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.0609 AC: 315 AN: 5176

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4822

European-Finnish (FIN) AF: 0.0345 AC: 364 AN: 10536

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4189 AN: 68004

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0654 Hom.: 713

Bravo AF: 0.0557

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.78
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs3862556; hg19: chr10-76540987;