rs268921

chr19-50919435-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 0.461 in 151,758 control chromosomes in the GnomAD database, including 17,409 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 0.46 (17409 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.461 AC: 69900 AN: 151640 Hom.: 17389 Cov.: 30

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.461 AC: 69964 AN: 151758 Hom.: 17409 Cov.: 30 AF XY: 0.458 AC XY: 33971 AN XY: 74158

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.432

Alfa AF: 0.421 Hom.: 1771

Bravo AF: 0.467

Asia WGS AF: 0.658 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.35
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs268921; hg19: chr19-51422691;