rs1701934

chr19-50897145-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;