chr6-32716252-C-G

Position:

• chr6-32716252-C-G

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 0.321 in 151,958 control chromosomes in the GnomAD database, including 8,929 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 0.32 (8929 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48769 AN: 151840 Hom.: 8911 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.321 AC: 48843 AN: 151958 Hom.: 8929 Cov.: 31 AF XY: 0.317 AC XY: 23558 AN XY: 74280

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.345

Alfa AF: 0.272 Hom.: 819

Bravo AF: 0.343

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6936863; hg19: chr6-32684029;