15-72998562-T-C

Position:

• chr15-72998562-T-C

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 0.112 in 152,198 control chromosomes in the GnomAD database, including 1,918 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 (1918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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: 0.112 AC: 17004 AN: 152080 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.112 AC: 17056 AN: 152198 Hom.: 1918 Cov.: 32 AF XY: 0.110 AC XY: 8158 AN XY: 74420

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.0386

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.0956

Alfa AF: 0.0441 Hom.: 169

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.053
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7174900; hg19: chr15-73290903;