5-25970557-A-G

Variant names:

• chr5-25970557-A-G
• rs7732252
• ENST00000658114.2:n.124+6607A>G

Variant summary

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

The ENST00000658114.2(ENSG00000286625):​n.124+6607A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,000 control chromosomes in the GnomAD database, including 9,539 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 0.34 (9539 hom., cov: 32)
• Consequence: ENSG00000286625 ENST00000658114.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 4 publications found

Genes affected

ENSG00000286625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658114.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286625	ENST00000658114.2		n.124+6607A>G		intron	N/A
	ENSG00000286625	ENST00000668718.1		n.49+6607A>G		intron	N/A
	ENSG00000286625	ENST00000759668.1		n.115+6607A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51068 AN: 151882 Hom.: 9516 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.336 AC: 51131 AN: 152000 Hom.: 9539 Cov.: 32 AF XY: 0.340 AC XY: 25214 AN XY: 74266

African (AFR) AF: 0.468 AC: 19394 AN: 41466

American (AMR) AF: 0.397 AC: 6060 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2522 AN: 5130

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3390 AN: 10574

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16719 AN: 67968

Other (OTH) AF: 0.324 AC: 685 AN: 2114

Alfa AF: 0.280 Hom.: 20839

Bravo AF: 0.354

Asia WGS AF: 0.379 AC: 1316 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.31
PhyloP100		0.13

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: rs7732252;

hg19: chr5-25970666;