6-31279542-T-C

Variant names:

• chr6-31279542-T-C
• rs12216025

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 0.126 in 152,172 control chromosomes in the GnomAD database, including 1,326 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 0.13 (1326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.974

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 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: 0.126 AC: 19190 AN: 152054 Hom.: 1326 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.126 AC: 19198 AN: 152172 Hom.: 1326 Cov.: 32 AF XY: 0.127 AC XY: 9431 AN XY: 74402

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0997

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.140

Alfa AF: 0.128 Hom.: 184

Bravo AF: 0.125

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12216025; hg19: chr6-31247319;