rs2157339

chr6-32543895-T-A

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 0.0623 in 145,388 control chromosomes in the GnomAD database, including 716 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 0.062 (716 hom., cov: 37)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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: 0.0622 AC: 9040 AN: 145274 Hom.: 715 Cov.: 37

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0433

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.0268

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0623 AC: 9055 AN: 145388 Hom.: 716 Cov.: 37 AF XY: 0.0607 AC XY: 4299 AN XY: 70844

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.0303

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.0477

Gnomad4 OTH AF: 0.0660

Alfa AF: 0.0590 Hom.: 61

Asia WGS AF: 0.0420 AC: 146 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.5
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157339; hg19: chr6-32511672;