rs1701934

Variant names:

• chr19-50897145-C-T
• rs1701934

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 0.127 in 152,020 control chromosomes in the GnomAD database, including 3,977 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 0.13 (3977 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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: 0.127 AC: 19256 AN: 151902 Hom.: 3949 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00208

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00478

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.127 AC: 19334 AN: 152020 Hom.: 3977 Cov.: 31 AF XY: 0.123 AC XY: 9131 AN XY: 74322

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.0531

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00208

Gnomad4 FIN AF: 0.000754

Gnomad4 NFE AF: 0.00476

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0766 Hom.: 305

Bravo AF: 0.146

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1701934; hg19: chr19-51400401;