rs7725288

Variant names:

• chr5-36328204-C-A
• rs7725288
• ENST00000756147.1:n.174+389C>A

Variant summary

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

The ENST00000756147.1(ENSG00000298515):​n.174+389C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,078 control chromosomes in the GnomAD database, including 26,724 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 0.58 (26724 hom., cov: 33)
• Consequence: ENSG00000298515 ENST00000756147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 6 publications found

Genes affected

ENSG00000298515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900962	XR_007058732.1	n.943+389C>A		intron_variant	Intron 2 of 3
LOC124900962	XR_007058733.1	n.299+389C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298515	ENST00000756147.1	n.174+389C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87707 AN: 151960 Hom.: 26681 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.577 AC: 87799 AN: 152078 Hom.: 26724 Cov.: 33 AF XY: 0.571 AC XY: 42448 AN XY: 74316

African (AFR) AF: 0.785 AC: 32584 AN: 41492

American (AMR) AF: 0.473 AC: 7224 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1474 AN: 5176

South Asian (SAS) AF: 0.399 AC: 1921 AN: 4810

European-Finnish (FIN) AF: 0.548 AC: 5792 AN: 10560

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35369 AN: 67984

Other (OTH) AF: 0.537 AC: 1136 AN: 2114

Alfa AF: 0.528 Hom.: 15126

Bravo AF: 0.577

Asia WGS AF: 0.373 AC: 1296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.3
DANN	Benign	0.72
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7725288; hg19: chr5-36328306;