chr6-31275182-C-T

Variant names:

• chr6-31275182-C-T
• rs2844615

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 0.114 in 152,242 control chromosomes in the GnomAD database, including 1,045 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 0.11 (1045 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 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: 0.114 AC: 17284 AN: 152122 Hom.: 1044 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.114 AC: 17284 AN: 152242 Hom.: 1045 Cov.: 33 AF XY: 0.108 AC XY: 8065 AN XY: 74424

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.121

Alfa AF: 0.128 Hom.: 116

Bravo AF: 0.120

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
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: rs2844615; hg19: chr6-31242959;