rs2402941

chr7-128922960-A-Gchr7-128922960-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 0.775 in 152,086 control chromosomes in the GnomAD database, including 46,789 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 0.78 (46789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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: 0.775 AC: 117846 AN: 151966 Hom.: 46776 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.775 AC: 117905 AN: 152086 Hom.: 46789 Cov.: 31 AF XY: 0.776 AC XY: 57665 AN XY: 74340

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.771

Alfa AF: 0.823 Hom.: 15263

Bravo AF: 0.756

Asia WGS AF: 0.710 AC: 2468 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	3.9
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: rs2402941; hg19: chr7-128563014;