rs17526278

chr19-50854631-G-Achr19-50854631-G-C

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 0.142 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.142 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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0743

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0779 Hom.: 133

Bravo AF: 0.155

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17526278; hg19: chr19-51357887;