15-77099261-C-T

Variant names:

• chr15-77099261-C-T
• rs12899474

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0298 AC: 1237 AN: 41562

American (AMR) AF: 0.0969 AC: 1483 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5184

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4830

European-Finnish (FIN) AF: 0.0975 AC: 1035 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6851 AN: 68008

Other (OTH) AF: 0.0724 AC: 153 AN: 2114

Alfa AF: 0.0901 Hom.: 846

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs12899474; hg19: chr15-77391603;