6-32715138-T-G

Variant names:

• chr6-32715138-T-G
• rs3997854

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 0.164 in 152,076 control chromosomes in the GnomAD database, including 2,417 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 0.16 (2417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.164 AC: 24938 AN: 151958 Hom.: 2415 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.164 AC: 24973 AN: 152076 Hom.: 2417 Cov.: 32 AF XY: 0.163 AC XY: 12143 AN XY: 74350

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0822

Gnomad4 SAS AF: 0.0664

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.146

Alfa AF: 0.112 Hom.: 662

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3997854; hg19: chr6-32682915;