rs161927

chr3-7796555-G-Achr3-7796555-G-C

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 0.808 in 151,972 control chromosomes in the GnomAD database, including 50,416 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 0.81 (50416 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.808 AC: 122750 AN: 151854 Hom.: 50391 Cov.: 30

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.808 AC: 122835 AN: 151972 Hom.: 50416 Cov.: 30 AF XY: 0.813 AC XY: 60385 AN XY: 74268

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.817

Alfa AF: 0.855 Hom.: 70765

Bravo AF: 0.797

Asia WGS AF: 0.893 AC: 3105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.012
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs161927; hg19: chr3-7838242;