5-1890763-G-A

Variant names:

• chr5-1890763-G-A
• rs12655062
• ENST00000514569.1:n.108+2481G>A

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+2481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,140 control chromosomes in the GnomAD database, including 7,835 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 0.30 (7835 hom., cov: 33)
• Consequence: CTD-2194D22.4 ENST00000514569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 4 publications found

Genes affected

CTD-2194D22.4 (HGNC:58994):

CTD-2194D22.4 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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+2481G>A		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+2481G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46250 AN: 152022 Hom.: 7825 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.304 AC: 46280 AN: 152140 Hom.: 7835 Cov.: 33 AF XY: 0.314 AC XY: 23340 AN XY: 74368

African (AFR) AF: 0.155 AC: 6428 AN: 41498

American (AMR) AF: 0.410 AC: 6268 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1769 AN: 5178

South Asian (SAS) AF: 0.362 AC: 1747 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4478 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23181 AN: 67980

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.318 Hom.: 16050

Bravo AF: 0.296

Asia WGS AF: 0.364 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.22

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: rs12655062;

hg19: chr5-1890877;