rs2219939

Variant names:

• chr15-78737381-G-A
• rs2219939

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 0.527 in 152,012 control chromosomes in the GnomAD database, including 25,663 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 0.53 (25663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80078 AN: 151894 Hom.: 25668 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.527 AC: 80068 AN: 152012 Hom.: 25663 Cov.: 32 AF XY: 0.518 AC XY: 38492 AN XY: 74304

African (AFR) AF: 0.199 AC: 8248 AN: 41456

American (AMR) AF: 0.461 AC: 7040 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2312 AN: 3468

East Asian (EAS) AF: 0.128 AC: 661 AN: 5180

South Asian (SAS) AF: 0.526 AC: 2525 AN: 4804

European-Finnish (FIN) AF: 0.598 AC: 6307 AN: 10548

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50967 AN: 67976

Other (OTH) AF: 0.548 AC: 1157 AN: 2110

Alfa AF: 0.615 Hom.: 4519

Bravo AF: 0.499

Asia WGS AF: 0.315 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.45
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2219939; hg19: chr15-79029723;