15-36565184-T-C

Variant names:

• chr15-36565184-T-C
• rs1377724

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 0.879 in 152,214 control chromosomes in the GnomAD database, including 58,908 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 0.88 (58908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.892 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: 0.879 AC: 133729 AN: 152096 Hom.: 58849 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.879 AC: 133848 AN: 152214 Hom.: 58908 Cov.: 31 AF XY: 0.879 AC XY: 65433 AN XY: 74434

African (AFR) AF: 0.899 AC: 37356 AN: 41530

American (AMR) AF: 0.900 AC: 13763 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3144 AN: 3472

East Asian (EAS) AF: 0.881 AC: 4543 AN: 5158

South Asian (SAS) AF: 0.853 AC: 4114 AN: 4822

European-Finnish (FIN) AF: 0.891 AC: 9446 AN: 10604

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58704 AN: 68022

Other (OTH) AF: 0.880 AC: 1857 AN: 2110

Alfa AF: 0.869 Hom.: 173112

Bravo AF: 0.883

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.24
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs1377724; hg19: chr15-36857385;