6-32627306-G-T

Variant names:

• chr6-32627306-G-T
• rs3129768

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 0.762 in 147,692 control chromosomes in the GnomAD database, including 43,425 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 0.76 (43425 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 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: 0.762 AC: 112453 AN: 147574 Hom.: 43398 Cov.: 26

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.855

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.762 AC: 112538 AN: 147692 Hom.: 43425 Cov.: 26 AF XY: 0.757 AC XY: 54574 AN XY: 72062

African (AFR) AF: 0.665 AC: 26512 AN: 39852

American (AMR) AF: 0.806 AC: 11887 AN: 14744

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3112 AN: 3424

East Asian (EAS) AF: 0.709 AC: 3568 AN: 5034

South Asian (SAS) AF: 0.710 AC: 3287 AN: 4632

European-Finnish (FIN) AF: 0.742 AC: 7469 AN: 10068

Middle Eastern (MID) AF: 0.846 AC: 242 AN: 286

European-Non Finnish (NFE) AF: 0.810 AC: 54015 AN: 66716

Other (OTH) AF: 0.804 AC: 1641 AN: 2042

Alfa AF: 0.792 Hom.: 97608

Bravo AF: 0.765

Asia WGS AF: 0.647 AC: 2252 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3129768; hg19: chr6-32595083;