19-23966743-C-T

Variant names:

• chr19-23966743-C-T
• rs2195987
• ENST00000849319.1:n.122+8358G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849319.1(ENSG00000269289):​n.122+8358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000269289 ENST00000849319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 12 publications found

Genes affected

ENSG00000269289 (HGNC:58110):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849319.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000269289	ENST00000849319.1		n.122+8358G>A		intron	N/A
	ENSG00000269289	ENST00000849320.1		n.100+7551G>A		intron	N/A

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

African (AFR) AF: 0.941 AC: 39091 AN: 41530

American (AMR) AF: 0.821 AC: 12553 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2699 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4534 AN: 5160

South Asian (SAS) AF: 0.819 AC: 3949 AN: 4820

European-Finnish (FIN) AF: 0.805 AC: 8525 AN: 10584

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52516 AN: 68002

Other (OTH) AF: 0.806 AC: 1706 AN: 2116

Alfa AF: 0.786 Hom.: 148132

Bravo AF: 0.836

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2195987; hg19: chr19-24149545;