chr5-36328204-C-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756147.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298515	ENST00000756147.1		n.174+389C>A		intron	N/A

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 v4.9

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;