chr6-31099232-T-C

Variant names:

• chr6-31099232-T-C
• rs2517403

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 0.368 in 151,776 control chromosomes in the GnomAD database, including 10,715 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 0.37 (10715 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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: 0.368 AC: 55837 AN: 151658 Hom.: 10703 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.0995

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.368 AC: 55880 AN: 151776 Hom.: 10715 Cov.: 31 AF XY: 0.365 AC XY: 27042 AN XY: 74164

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.0998

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.403

Alfa AF: 0.356 Hom.: 7598

Bravo AF: 0.373

Asia WGS AF: 0.247 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517403; hg19: chr6-31067009;