15-31471406-T-G

Position:

• chr15-31471406-T-G

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 0.256 in 152,048 control chromosomes in the GnomAD database, including 5,489 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 0.26 (5489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38841 AN: 151930 Hom.: 5486 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.256 AC: 38854 AN: 152048 Hom.: 5489 Cov.: 32 AF XY: 0.255 AC XY: 18981 AN XY: 74338

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.275

Alfa AF: 0.244 Hom.: 1293

Bravo AF: 0.264

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11071075; hg19: chr15-31763609;