rs2015279

Variant names:

• chr19-29118193-C-T
• rs2015279

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 0.272 in 152,062 control chromosomes in the GnomAD database, including 6,377 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 0.27 (6377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 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: 0.273 AC: 41418 AN: 151944 Hom.: 6373 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.272 AC: 41412 AN: 152062 Hom.: 6377 Cov.: 32 AF XY: 0.270 AC XY: 20087 AN XY: 74330

African (AFR) AF: 0.123 AC: 5086 AN: 41510

American (AMR) AF: 0.259 AC: 3955 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1570 AN: 5146

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4816

European-Finnish (FIN) AF: 0.291 AC: 3082 AN: 10578

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23716 AN: 67960

Other (OTH) AF: 0.309 AC: 649 AN: 2102

Alfa AF: 0.317 Hom.: 2861

Bravo AF: 0.260

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.26
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2015279; hg19: chr19-29609100;