15-86072147-T-C

Variant names:

• chr15-86072147-T-C
• rs2120640

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 0.828 in 152,210 control chromosomes in the GnomAD database, including 52,859 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 0.83 (52859 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 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: 0.828 AC: 125898 AN: 152092 Hom.: 52832 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.828 AC: 125975 AN: 152210 Hom.: 52859 Cov.: 33 AF XY: 0.831 AC XY: 61858 AN XY: 74430

African (AFR) AF: 0.687 AC: 28525 AN: 41494

American (AMR) AF: 0.881 AC: 13468 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2962 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4084 AN: 5178

South Asian (SAS) AF: 0.727 AC: 3505 AN: 4818

European-Finnish (FIN) AF: 0.941 AC: 9990 AN: 10618

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60544 AN: 68020

Other (OTH) AF: 0.840 AC: 1774 AN: 2112

Alfa AF: 0.871 Hom.: 91211

Bravo AF: 0.817

Asia WGS AF: 0.751 AC: 2609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2120640; hg19: chr15-86615378;