chr6-32626411-A-T

Position:

• chr6-32626411-A-T

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 0.273 in 150,958 control chromosomes in the GnomAD database, including 6,023 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 0.27 (6023 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

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 = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41142 AN: 150842 Hom.: 6021 Cov.: 29

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.273 AC: 41171 AN: 150958 Hom.: 6023 Cov.: 29 AF XY: 0.270 AC XY: 19894 AN XY: 73712

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271768; hg19: chr6-32594188; COSMIC: COSV70073327;