6-32714947-C-T

Variant names:

• chr6-32714947-C-T
• rs3873444

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 0.143 in 152,148 control chromosomes in the GnomAD database, including 1,892 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 0.14 (1892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.143 AC: 21785 AN: 152030 Hom.: 1888 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.143 AC: 21823 AN: 152148 Hom.: 1892 Cov.: 32 AF XY: 0.141 AC XY: 10507 AN XY: 74394

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.161

Alfa AF: 0.110 Hom.: 1601

Bravo AF: 0.147

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3873444; hg19: chr6-32682724;