chr19-51724663-C-T

Variant names:

• chr19-51724663-C-T
• rs11672222

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 0.752 in 151,838 control chromosomes in the GnomAD database, including 43,238 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 0.75 (43238 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.752 AC: 114078 AN: 151720 Hom.: 43184 Cov.: 30

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.752 AC: 114186 AN: 151838 Hom.: 43238 Cov.: 30 AF XY: 0.757 AC XY: 56134 AN XY: 74170

African (AFR) AF: 0.739 AC: 30574 AN: 41350

American (AMR) AF: 0.797 AC: 12161 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2296 AN: 3470

East Asian (EAS) AF: 0.990 AC: 5065 AN: 5118

South Asian (SAS) AF: 0.833 AC: 4019 AN: 4822

European-Finnish (FIN) AF: 0.796 AC: 8408 AN: 10562

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49410 AN: 67942

Other (OTH) AF: 0.739 AC: 1561 AN: 2112

Alfa AF: 0.734 Hom.: 70261

Bravo AF: 0.751

Asia WGS AF: 0.913 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.93
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs11672222; hg19: chr19-52227916; COSMIC: COSV55786336;