rs3740051

Variant names:

• chr10-67884201-A-G
• rs3740051

Your query was ambiguous. Multiple possible variants found:

• chr10-67884201-A-G
• chr10-67884201-A-T

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 0.0733 in 152,236 control chromosomes in the GnomAD database, including 679 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 0.073 (679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 50 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11160 AN: 152118 Hom.: 678 Cov.: 33

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0733 AC: 11156 AN: 152236 Hom.: 679 Cov.: 33 AF XY: 0.0789 AC XY: 5874 AN XY: 74416

African (AFR) AF: 0.0226 AC: 941 AN: 41576

American (AMR) AF: 0.113 AC: 1728 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1480 AN: 5170

South Asian (SAS) AF: 0.129 AC: 624 AN: 4830

European-Finnish (FIN) AF: 0.146 AC: 1551 AN: 10588

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4465 AN: 68020

Other (OTH) AF: 0.0691 AC: 146 AN: 2114

Alfa AF: 0.0349 Hom.: 33

Bravo AF: 0.0694

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.86
PromoterAI		0.062	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3740051; hg19: chr10-69643959;