6-32839676-A-G

Variant names:

• chr6-32839676-A-G
• rs3763365

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 0.474 in 151,772 control chromosomes in the GnomAD database, including 17,296 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 0.47 (17296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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: 0.475 AC: 71965 AN: 151654 Hom.: 17292 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.474 AC: 71992 AN: 151772 Hom.: 17296 Cov.: 32 AF XY: 0.474 AC XY: 35115 AN XY: 74150

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.469

Alfa AF: 0.479 Hom.: 4551

Bravo AF: 0.474

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763365; hg19: chr6-32807453;