15-72994811-T-G

Variant names:

• chr15-72994811-T-G
• rs7172316

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 0.115 in 151,998 control chromosomes in the GnomAD database, including 2,048 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 0.12 (2048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245

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 = 0.297 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: 0.115 AC: 17428 AN: 151880 Hom.: 2040 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0542

Gnomad SAS AF: 0.0384

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.115 AC: 17483 AN: 151998 Hom.: 2048 Cov.: 32 AF XY: 0.113 AC XY: 8364 AN XY: 74276

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0396

Gnomad4 OTH AF: 0.0981

Alfa AF: 0.0498 Hom.: 630

Bravo AF: 0.124

Asia WGS AF: 0.0850 AC: 295 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7172316; hg19: chr15-73287152;