6-32611226-T-C

Variant names:

• chr6-32611226-T-C
• rs502055

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 0.315 in 149,224 control chromosomes in the GnomAD database, including 7,681 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 0.31 (7681 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 30 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 (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.315 AC: 46922 AN: 149104 Hom.: 7671 Cov.: 26

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.315 AC: 46966 AN: 149224 Hom.: 7681 Cov.: 26 AF XY: 0.312 AC XY: 22730 AN XY: 72772

African (AFR) AF: 0.384 AC: 15493 AN: 40390

American (AMR) AF: 0.282 AC: 4198 AN: 14888

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1096 AN: 3432

East Asian (EAS) AF: 0.385 AC: 1931 AN: 5020

South Asian (SAS) AF: 0.341 AC: 1594 AN: 4680

European-Finnish (FIN) AF: 0.225 AC: 2298 AN: 10194

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19345 AN: 67398

Other (OTH) AF: 0.340 AC: 691 AN: 2034

Alfa AF: 0.315 Hom.: 2355

Bravo AF: 0.317

Asia WGS AF: 0.319 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.33
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs502055; hg19: chr6-32579003;