chr15-99534676-G-T

Variant names:

• chr15-99534676-G-T
• rs4313794

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 0.855 in 152,060 control chromosomes in the GnomAD database, including 55,925 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 0.86 (55925 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.906 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: 0.855 AC: 129934 AN: 151942 Hom.: 55889 Cov.: 31

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.855 AC: 130024 AN: 152060 Hom.: 55925 Cov.: 31 AF XY: 0.859 AC XY: 63824 AN XY: 74308

African (AFR) AF: 0.756 AC: 31336 AN: 41426

American (AMR) AF: 0.918 AC: 14027 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3047 AN: 3466

East Asian (EAS) AF: 0.804 AC: 4166 AN: 5180

South Asian (SAS) AF: 0.884 AC: 4259 AN: 4818

European-Finnish (FIN) AF: 0.945 AC: 9987 AN: 10568

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60271 AN: 68006

Other (OTH) AF: 0.867 AC: 1835 AN: 2116

Alfa AF: 0.882 Hom.: 72890

Bravo AF: 0.848

Asia WGS AF: 0.840 AC: 2918 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4313794; hg19: chr15-100074881;