rs186715

Variant names:

• chr19-6878125-T-G
• rs186715

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 0.548 in 151,816 control chromosomes in the GnomAD database, including 24,444 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 0.55 (24444 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 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: 0.548 AC: 83102 AN: 151698 Hom.: 24392 Cov.: 30

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.548 AC: 83214 AN: 151816 Hom.: 24444 Cov.: 30 AF XY: 0.547 AC XY: 40559 AN XY: 74194

African (AFR) AF: 0.782 AC: 32398 AN: 41412

American (AMR) AF: 0.494 AC: 7529 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1566 AN: 5128

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4808

European-Finnish (FIN) AF: 0.512 AC: 5395 AN: 10540

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30971 AN: 67904

Other (OTH) AF: 0.532 AC: 1119 AN: 2102

Alfa AF: 0.490 Hom.: 3776

Bravo AF: 0.558

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.55
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs186715; hg19: chr19-6878136;