6-32611226-T-C

Variant names:

• chr6-32611226-T-C
• rs502055

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 0.315 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.315 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

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.340

Alfa AF: 0.314 Hom.: 1029

Bravo AF: 0.317

Asia WGS AF: 0.319 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502055; hg19: chr6-32579003;