19-19274602-T-C

Variant names:

• chr19-19274602-T-C
• rs735273

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 0.419 in 151,924 control chromosomes in the GnomAD database, including 14,731 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 0.42 (14731 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.615 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: 0.418 AC: 63461 AN: 151806 Hom.: 14671 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.419 AC: 63588 AN: 151924 Hom.: 14731 Cov.: 31 AF XY: 0.415 AC XY: 30808 AN XY: 74252

African (AFR) AF: 0.621 AC: 25711 AN: 41408

American (AMR) AF: 0.412 AC: 6298 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1656 AN: 5152

South Asian (SAS) AF: 0.472 AC: 2269 AN: 4812

European-Finnish (FIN) AF: 0.232 AC: 2457 AN: 10580

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22673 AN: 67918

Other (OTH) AF: 0.415 AC: 875 AN: 2108

Alfa AF: 0.352 Hom.: 8086

Bravo AF: 0.439

Asia WGS AF: 0.445 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs735273; hg19: chr19-19385411;