rs2569531

chr19-50903362-A-Gchr19-50903362-A-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 0.451 in 151,750 control chromosomes in the GnomAD database, including 17,255 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 0.45 (17255 hom., cov: 30)
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.451 AC: 68320 AN: 151632 Hom.: 17226 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.451 AC: 68399 AN: 151750 Hom.: 17255 Cov.: 30 AF XY: 0.446 AC XY: 33049 AN XY: 74136

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.442

Alfa AF: 0.401 Hom.: 1626

Bravo AF: 0.464

Asia WGS AF: 0.322 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569531; hg19: chr19-51406618;