6-32696074-C-T

Variant names:

• chr6-32696074-C-T
• rs6457617

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 0.519 in 151,726 control chromosomes in the GnomAD database, including 20,897 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 0.52 (20897 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 165 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.619 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: 0.519 AC: 78663 AN: 151608 Hom.: 20873 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.519 AC: 78745 AN: 151726 Hom.: 20897 Cov.: 31 AF XY: 0.522 AC XY: 38686 AN XY: 74130

African (AFR) AF: 0.494 AC: 20430 AN: 41346

American (AMR) AF: 0.629 AC: 9596 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3464

East Asian (EAS) AF: 0.566 AC: 2915 AN: 5154

South Asian (SAS) AF: 0.378 AC: 1816 AN: 4804

European-Finnish (FIN) AF: 0.582 AC: 6104 AN: 10480

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33804 AN: 67916

Other (OTH) AF: 0.544 AC: 1148 AN: 2112

Alfa AF: 0.514 Hom.: 74094

Bravo AF: 0.528

Asia WGS AF: 0.532 AC: 1854 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	5.6
DANN	Benign	0.47
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs6457617; hg19: chr6-32663851; COSMIC: COSV65415058;