rs2569753

Variant names:

• chr19-50840922-T-C
• rs2569753
• ENST00000598079.1:n.213+9629T>C

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.213+9629T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,022 control chromosomes in the GnomAD database, including 18,501 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 0.47 (18501 hom., cov: 31)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598079.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105372441	NR_131203.1		n.213+9629T>C		intron	N/A
	LOC105372441	NR_131205.1		n.230+9629T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267968	ENST00000598079.1	TSL:3	n.213+9629T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71587 AN: 151902 Hom.: 18498 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.471 AC: 71599 AN: 152022 Hom.: 18501 Cov.: 31 AF XY: 0.470 AC XY: 34904 AN XY: 74298

African (AFR) AF: 0.276 AC: 11465 AN: 41470

American (AMR) AF: 0.382 AC: 5831 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1861 AN: 5166

South Asian (SAS) AF: 0.576 AC: 2771 AN: 4810

European-Finnish (FIN) AF: 0.540 AC: 5708 AN: 10570

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40303 AN: 67938

Other (OTH) AF: 0.504 AC: 1066 AN: 2116

Alfa AF: 0.518 Hom.: 2643

Bravo AF: 0.445

Asia WGS AF: 0.436 AC: 1518 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	0.61
DANN	Benign	0.48
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2569753;

hg19: chr19-51344178;