rs3763743

Variant names:

• chr10-59909293-T-C
• rs3763743

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 0.172 in 152,208 control chromosomes in the GnomAD database, including 2,876 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 0.17 (2876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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: 0.172 AC: 26120 AN: 152090 Hom.: 2880 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.172 AC: 26116 AN: 152208 Hom.: 2876 Cov.: 32 AF XY: 0.168 AC XY: 12537 AN XY: 74412

African (AFR) AF: 0.0492 AC: 2044 AN: 41546

American (AMR) AF: 0.167 AC: 2548 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3468

East Asian (EAS) AF: 0.0366 AC: 190 AN: 5190

South Asian (SAS) AF: 0.206 AC: 995 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1909 AN: 10588

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16962 AN: 67990

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.193 Hom.: 421

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.92
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs3763743; hg19: chr10-61669051;