rs1878926

Variant names:

• chr19-36439619-T-C
• rs1878926

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 0.54 in 151,982 control chromosomes in the GnomAD database, including 22,506 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 0.54 (22506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 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: 0.540 AC: 82043 AN: 151864 Hom.: 22484 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.540 AC: 82114 AN: 151982 Hom.: 22506 Cov.: 31 AF XY: 0.538 AC XY: 39952 AN XY: 74290

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.522

Alfa AF: 0.570 Hom.: 13034

Bravo AF: 0.524

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	7.4
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878926; hg19: chr19-36930521;