chr6-32840455-A-G

Variant names:

• chr6-32840455-A-G
• rs3763349

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 0.529 in 152,024 control chromosomes in the GnomAD database, including 21,509 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 0.53 (21509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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: 0.529 AC: 80377 AN: 151906 Hom.: 21482 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.529 AC: 80444 AN: 152024 Hom.: 21509 Cov.: 32 AF XY: 0.525 AC XY: 39001 AN XY: 74316

African (AFR) AF: 0.571 AC: 23690 AN: 41484

American (AMR) AF: 0.534 AC: 8136 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3470

East Asian (EAS) AF: 0.509 AC: 2628 AN: 5162

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4822

European-Finnish (FIN) AF: 0.458 AC: 4839 AN: 10570

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34995 AN: 67948

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.525 Hom.: 88216

Bravo AF: 0.536

Asia WGS AF: 0.523 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs3763349; hg19: chr6-32808232;