rs1701930

Variant names:

• chr19-50916290-A-G
• rs1701930

Your query was ambiguous. Multiple possible variants found:

• chr19-50916290-A-G
• chr19-50916290-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.593 in 151,972 control chromosomes in the GnomAD database, including 27,813 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 0.59 (27813 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90032 AN: 151854 Hom.: 27761 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.593 AC: 90150 AN: 151972 Hom.: 27813 Cov.: 31 AF XY: 0.592 AC XY: 43921 AN XY: 74246

African (AFR) AF: 0.669 AC: 27754 AN: 41464

American (AMR) AF: 0.711 AC: 10855 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3466

East Asian (EAS) AF: 0.102 AC: 527 AN: 5156

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4812

European-Finnish (FIN) AF: 0.563 AC: 5940 AN: 10556

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38800 AN: 67940

Other (OTH) AF: 0.592 AC: 1250 AN: 2112

Alfa AF: 0.596 Hom.: 52082

Bravo AF: 0.609

Asia WGS AF: 0.325 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1701930; hg19: chr19-51419546;