rs3740051

chr10-67884201-A-Gchr10-67884201-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0109 Hom.: 6

Bravo AF: 0.0694

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	2.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3740051; hg19: chr10-69643959;