rs17526278

Variant names:

• chr19-50854631-G-A
• rs17526278

Your query was ambiguous. Multiple possible variants found:

• chr19-50854631-G-A
• chr19-50854631-G-C

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 0.142 in 151,920 control chromosomes in the GnomAD database, including 2,085 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 0.14 (2085 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.42
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21489 AN: 151802 Hom.: 2079 Cov.: 30

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.142 AC: 21517 AN: 151920 Hom.: 2085 Cov.: 30 AF XY: 0.138 AC XY: 10245 AN XY: 74284

African (AFR) AF: 0.272 AC: 11263 AN: 41346

American (AMR) AF: 0.110 AC: 1680 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3472

East Asian (EAS) AF: 0.0743 AC: 383 AN: 5154

South Asian (SAS) AF: 0.0478 AC: 230 AN: 4812

European-Finnish (FIN) AF: 0.0484 AC: 513 AN: 10598

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0971 AC: 6598 AN: 67948

Other (OTH) AF: 0.144 AC: 303 AN: 2108

Alfa AF: 0.0983 Hom.: 369

Bravo AF: 0.155

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.51
PhyloP100		-4.4
PromoterAI		-0.028	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17526278; hg19: chr19-51357887;