rs1879894

Variant names:

• chr15-79976477-C-T
• rs1879894

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 0.34 in 152,088 control chromosomes in the GnomAD database, including 9,099 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 0.34 (9099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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: 0.340 AC: 51719 AN: 151970 Hom.: 9085 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.340 AC: 51757 AN: 152088 Hom.: 9099 Cov.: 32 AF XY: 0.341 AC XY: 25344 AN XY: 74348

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.337

Alfa AF: 0.331 Hom.: 6098

Bravo AF: 0.347

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879894; hg19: chr15-80268819;