chr6-32225901-G-A

Variant names:

• chr6-32225901-G-A
• rs479536

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 0.0493 in 152,210 control chromosomes in the GnomAD database, including 253 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 0.049 (253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0723 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: 0.0493 AC: 7497 AN: 152092 Hom.: 253 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.00500

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0493 AC: 7497 AN: 152210 Hom.: 253 Cov.: 32 AF XY: 0.0458 AC XY: 3405 AN XY: 74418

African (AFR) AF: 0.0385 AC: 1600 AN: 41520

American (AMR) AF: 0.0759 AC: 1161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4824

European-Finnish (FIN) AF: 0.00500 AC: 53 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4235 AN: 68016

Other (OTH) AF: 0.0578 AC: 122 AN: 2112

Alfa AF: 0.0541 Hom.: 664

Bravo AF: 0.0560

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs479536; hg19: chr6-32193678;