chr6-32477914-C-T

Variant names:

• chr6-32477914-C-T
• rs9378212

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;