chr15-40145919-G-A

Variant names:

• chr15-40145919-G-A
• rs1565863

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 0.563 in 152,080 control chromosomes in the GnomAD database, including 26,339 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 0.56 (26339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85565 AN: 151962 Hom.: 26335 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.563 AC: 85599 AN: 152080 Hom.: 26339 Cov.: 32 AF XY: 0.560 AC XY: 41628 AN XY: 74340

African (AFR) AF: 0.329 AC: 13658 AN: 41460

American (AMR) AF: 0.570 AC: 8711 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2041 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5170

South Asian (SAS) AF: 0.518 AC: 2495 AN: 4820

European-Finnish (FIN) AF: 0.700 AC: 7412 AN: 10584

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47839 AN: 67988

Other (OTH) AF: 0.537 AC: 1134 AN: 2112

Alfa AF: 0.653 Hom.: 126937

Bravo AF: 0.542

Asia WGS AF: 0.381 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.38
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1565863; hg19: chr15-40438120;