chr19-50919435-G-C

Variant names:

• chr19-50919435-G-C
• rs268921

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 0.461 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.616 AC: 25492 AN: 41402

American (AMR) AF: 0.351 AC: 5348 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4197 AN: 5116

South Asian (SAS) AF: 0.536 AC: 2563 AN: 4786

European-Finnish (FIN) AF: 0.356 AC: 3745 AN: 10528

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26003 AN: 67884

Other (OTH) AF: 0.432 AC: 913 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.46
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs268921; hg19: chr19-51422691;