rs172310

chr7-155822933-A-Cchr7-155822933-A-Gchr7-155822933-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 0.742 in 152,058 control chromosomes in the GnomAD database, including 42,323 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 0.74 (42323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.742 AC: 112737 AN: 151940 Hom.: 42263 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.742 AC: 112858 AN: 152058 Hom.: 42323 Cov.: 32 AF XY: 0.741 AC XY: 55083 AN XY: 74300

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.721

Alfa AF: 0.700 Hom.: 49557

Bravo AF: 0.748

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.0030
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs172310; hg19: chr7-155615627;