chr6-32477914-C-T

Position:

• chr6-32477914-C-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 0.384 in 149,372 control chromosomes in the GnomAD database, including 11,693 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 0.38 (11693 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 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: 0.384 AC: 57333 AN: 149256 Hom.: 11686 Cov.: 36

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.384 AC: 57371 AN: 149372 Hom.: 11693 Cov.: 36 AF XY: 0.384 AC XY: 28042 AN XY: 73048

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.389

Alfa AF: 0.405 Hom.: 3574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9378212; hg19: chr6-32445691;