19-23966743-C-T

Variant names:

• chr19-23966743-C-T
• rs2195987

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.832 in 152,180 control chromosomes in the GnomAD database, including 53,103 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 0.83 (53103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 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: 0.832 AC: 126519 AN: 152062 Hom.: 53047 Cov.: 32

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.832 AC: 126632 AN: 152180 Hom.: 53103 Cov.: 32 AF XY: 0.833 AC XY: 61960 AN XY: 74378

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.806

Alfa AF: 0.777 Hom.: 64205

Bravo AF: 0.836

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2195987; hg19: chr19-24149545;