rs161339

Variant names:

• chr7-137370779-A-G
• rs161339

Your query was ambiguous. Multiple possible variants found:

• chr7-137370779-A-G
• chr7-137370779-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 0.0836 in 152,220 control chromosomes in the GnomAD database, including 719 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 0.084 (719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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: 0.0837 AC: 12727 AN: 152102 Hom.: 719 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0836 AC: 12727 AN: 152220 Hom.: 719 Cov.: 32 AF XY: 0.0838 AC XY: 6239 AN XY: 74432

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.0733

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0849

Alfa AF: 0.0739 Hom.: 468

Bravo AF: 0.0853

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs161339; hg19: chr7-137055525;