19-38645234-C-T

Variant names:

• chr19-38645234-C-T
• rs12052046

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 0.117 in 152,140 control chromosomes in the GnomAD database, including 1,231 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 0.12 (1231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.117 AC: 17861 AN: 152022 Hom.: 1230 Cov.: 32

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.117 AC: 17867 AN: 152140 Hom.: 1231 Cov.: 32 AF XY: 0.118 AC XY: 8743 AN XY: 74364

African (AFR) AF: 0.0668 AC: 2773 AN: 41510

American (AMR) AF: 0.127 AC: 1946 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.00810 AC: 42 AN: 5182

South Asian (SAS) AF: 0.142 AC: 682 AN: 4808

European-Finnish (FIN) AF: 0.137 AC: 1445 AN: 10584

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9658 AN: 67998

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.134 Hom.: 5729

Bravo AF: 0.114

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.71
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12052046; hg19: chr19-39135874;