rs25531

Variant names:

• chr17-30237328-T-C
• rs25531
• ENST00000724731.1:n.109+258T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-30237328-T-C
• chr17-30237328-T-G

Variant summary

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

The ENST00000724731.1(ENSG00000266120):​n.109+258T>C 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 0.19 (468 hom., cov: 4)
• Consequence: ENSG00000266120 ENST00000724731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 749 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.280+258T>C		intron_variant	Intron 1 of 3
LOC105371720	XR_007065695.1	n.-170T>C		upstream_gene_variant
LOC105371720	XR_007065696.1	n.-170T>C		upstream_gene_variant
LOC105371720	XR_007065698.1	n.-170T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000724731.1	n.109+258T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 5881 AN: 31434 Hom.: 464 Cov.: 4

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0938

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.187 AC: 5896 AN: 31456 Hom.: 468 Cov.: 4 AF XY: 0.196 AC XY: 2750 AN XY: 13996

African (AFR) AF: 0.293 AC: 2651 AN: 9038

American (AMR) AF: 0.179 AC: 344 AN: 1918

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 72 AN: 844

East Asian (EAS) AF: 0.321 AC: 193 AN: 602

South Asian (SAS) AF: 0.292 AC: 158 AN: 542

European-Finnish (FIN) AF: 0.192 AC: 215 AN: 1120

Middle Eastern (MID) AF: 0.100 AC: 3 AN: 30

European-Non Finnish (NFE) AF: 0.129 AC: 2161 AN: 16750

Other (OTH) AF: 0.186 AC: 75 AN: 404

Alfa AF: 0.0264 Hom.: 20

Bravo AF: 0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.5
DANN	Benign	0.41
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs25531; hg19: chr17-28564346;