19-23294911-C-T

Variant names:

• chr19-23294911-C-T
• rs167153

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 0.23 in 152,070 control chromosomes in the GnomAD database, including 4,614 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 0.23 (4614 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.229 AC: 34859 AN: 151952 Hom.: 4602 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.230 AC: 34917 AN: 152070 Hom.: 4614 Cov.: 32 AF XY: 0.226 AC XY: 16779 AN XY: 74340

African (AFR) AF: 0.366 AC: 15149 AN: 41446

American (AMR) AF: 0.132 AC: 2023 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3468

East Asian (EAS) AF: 0.153 AC: 790 AN: 5158

South Asian (SAS) AF: 0.232 AC: 1121 AN: 4822

European-Finnish (FIN) AF: 0.166 AC: 1761 AN: 10584

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12692 AN: 67996

Other (OTH) AF: 0.207 AC: 437 AN: 2108

Alfa AF: 0.161 Hom.: 635

Bravo AF: 0.232

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.32
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs167153; hg19: chr19-23477713; COSMIC: COSV74075427;