rs25532

Variant names:

• chr17-30237152-G-A
• rs25532
• ENST00000724731.1:n.109+82G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-30237152-G-A
• chr17-30237152-G-C
• chr17-30237152-G-T

Variant summary

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

The ENST00000724731.1(ENSG00000266120):​n.109+82G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.063 (318 hom., cov: 9)
• Consequence: ENSG00000266120 ENST00000724731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 57 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.280+82G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000724731.1	n.109+82G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 4113 AN: 65304 Hom.: 318 Cov.: 9

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0930

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.000842

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0215

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0629 AC: 4111 AN: 65326 Hom.: 318 Cov.: 9 AF XY: 0.0588 AC XY: 1824 AN XY: 31030

African (AFR) AF: 0.0135 AC: 208 AN: 15356

American (AMR) AF: 0.0326 AC: 256 AN: 7844

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 148 AN: 1816

East Asian (EAS) AF: 0.000845 AC: 2 AN: 2368

South Asian (SAS) AF: 0.0412 AC: 63 AN: 1530

European-Finnish (FIN) AF: 0.0672 AC: 289 AN: 4302

Middle Eastern (MID) AF: 0.0230 AC: 4 AN: 174

European-Non Finnish (NFE) AF: 0.100 AC: 3067 AN: 30652

Other (OTH) AF: 0.0418 AC: 37 AN: 886

Alfa AF: 0.116 Hom.: 1720

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs25532; hg19: chr17-28564170;