chr15-77099261-C-T

Position:

• chr15-77099261-C-T

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 0.0751 in 152,288 control chromosomes in the GnomAD database, including 537 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 0.075 (537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

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 (NFE) allele frequency at 95% confidence interval = 0.0987 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: 0.0751 AC: 11422 AN: 152170 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0751 AC: 11432 AN: 152288 Hom.: 537 Cov.: 32 AF XY: 0.0746 AC XY: 5554 AN XY: 74462

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0921 Hom.: 673

Bravo AF: 0.0736

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12899474; hg19: chr15-77391603;