rs1701926

Variant names:

• chr19-50905502-G-T
• rs1701926

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 0.85 in 152,198 control chromosomes in the GnomAD database, including 56,226 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 0.85 (56226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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: 0.850 AC: 129230 AN: 152080 Hom.: 56176 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.850 AC: 129340 AN: 152198 Hom.: 56226 Cov.: 32 AF XY: 0.844 AC XY: 62825 AN XY: 74396

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.868

Alfa AF: 0.858 Hom.: 7022

Bravo AF: 0.852

Asia WGS AF: 0.525 AC: 1830 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	0.58
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1701926; hg19: chr19-51408758;