6-132574108-T-G

Variant names:

• chr6-132574108-T-G
• rs6912930

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.573 in 152,038 control chromosomes in the GnomAD database, including 25,556 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 0.57 (25556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87104 AN: 151918 Hom.: 25528 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.573 AC: 87179 AN: 152038 Hom.: 25556 Cov.: 32 AF XY: 0.571 AC XY: 42399 AN XY: 74300

African (AFR) AF: 0.630 AC: 26132 AN: 41480

American (AMR) AF: 0.551 AC: 8423 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1652 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1432 AN: 5166

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4814

European-Finnish (FIN) AF: 0.621 AC: 6548 AN: 10550

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39136 AN: 67976

Other (OTH) AF: 0.526 AC: 1108 AN: 2108

Alfa AF: 0.463 Hom.: 1297

Bravo AF: 0.570

Asia WGS AF: 0.377 AC: 1314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.57
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6912930; hg19: chr6-132895247;