19-53309270-T-C

Variant names:

• chr19-53309270-T-C
• rs1428642

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 0.502 in 151,886 control chromosomes in the GnomAD database, including 19,291 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 0.50 (19291 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76128 AN: 151770 Hom.: 19280 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.502 AC: 76178 AN: 151886 Hom.: 19291 Cov.: 33 AF XY: 0.498 AC XY: 37006 AN XY: 74256

African (AFR) AF: 0.449 AC: 18612 AN: 41466

American (AMR) AF: 0.470 AC: 7179 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2415 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2000 AN: 5142

South Asian (SAS) AF: 0.444 AC: 2135 AN: 4810

European-Finnish (FIN) AF: 0.535 AC: 5613 AN: 10492

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36321 AN: 67916

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.526 Hom.: 10948

Bravo AF: 0.497

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.4
DANN	Benign	0.11
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1428642; hg19: chr19-53812523;