ENST00000514569.1:n.108+3425A>G

Variant names:

• chr5-1891707-A-G
• rs10866528
• ENST00000514569.1:n.108+3425A>G

Variant summary

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

The ENST00000514569.1(CTD-2194D22.4):​n.108+3425A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,890 control chromosomes in the GnomAD database, including 17,521 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 0.48 (17521 hom., cov: 33)
• Consequence: CTD-2194D22.4 ENST00000514569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 8 publications found

Genes affected

CTD-2194D22.4 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514569.1. 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
	CTD-2194D22.4	NR_109912.1		n.109+3425A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTD-2194D22.4	ENST00000514569.1	TSL:1	n.108+3425A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72658 AN: 151772 Hom.: 17503 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.479 AC: 72722 AN: 151890 Hom.: 17521 Cov.: 33 AF XY: 0.484 AC XY: 35917 AN XY: 74230

African (AFR) AF: 0.468 AC: 19372 AN: 41380

American (AMR) AF: 0.518 AC: 7902 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1831 AN: 5150

South Asian (SAS) AF: 0.515 AC: 2475 AN: 4804

European-Finnish (FIN) AF: 0.522 AC: 5521 AN: 10578

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32347 AN: 67940

Other (OTH) AF: 0.493 AC: 1040 AN: 2108

Alfa AF: 0.481 Hom.: 8298

Bravo AF: 0.476

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.21
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10866528; hg19: chr5-1891821;