rs2158906

chr17-71261692-G-Achr17-71261692-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 0.628 in 151,996 control chromosomes in the GnomAD database, including 32,980 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 0.63 (32980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 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: 0.628 AC: 95414 AN: 151880 Hom.: 32969 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.628 AC: 95444 AN: 151996 Hom.: 32980 Cov.: 32 AF XY: 0.633 AC XY: 47043 AN XY: 74280

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.638

Alfa AF: 0.740 Hom.: 83778

Bravo AF: 0.601

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	13
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2158906; hg19: chr17-69257833;