chr6-32232370-C-G

Position:

• chr6-32232370-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 0.336 in 147,438 control chromosomes in the GnomAD database, including 8,800 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 0.34 (8800 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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: 0.336 AC: 49477 AN: 147320 Hom.: 8794 Cov.: 25

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.448

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.336 AC: 49518 AN: 147438 Hom.: 8800 Cov.: 25 AF XY: 0.335 AC XY: 23937 AN XY: 71422

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.406

Alfa AF: 0.166 Hom.: 320

Bravo AF: 0.347

Asia WGS AF: 0.427 AC: 1479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134926; hg19: chr6-32200147;