rs2219939

Positions:

• chr15-78737381-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.548

Alfa AF: 0.631 Hom.: 4501

Bravo AF: 0.499

Asia WGS AF: 0.315 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2219939; hg19: chr15-79029723;