6-32792937-G-T

Variant names:

• chr6-32792937-G-T
• rs2157082

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 0.614 in 151,976 control chromosomes in the GnomAD database, including 28,886 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 0.61 (28886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 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: 0.615 AC: 93317 AN: 151858 Hom.: 28871 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.614 AC: 93371 AN: 151976 Hom.: 28886 Cov.: 32 AF XY: 0.620 AC XY: 46031 AN XY: 74290

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.613

Alfa AF: 0.565 Hom.: 6310

Bravo AF: 0.606

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157082; hg19: chr6-32760714;