ENST00000658114.2:n.124+6607A>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901176	XR_007059127.1	n.58+6607A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286625	ENST00000658114.2	n.124+6607A>G		intron_variant	Intron 1 of 1
ENSG00000286625	ENST00000668718.1	n.49+6607A>G		intron_variant	Intron 1 of 1
ENSG00000286625	ENST00000759668.1	n.115+6607A>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7732252; hg19: chr5-25970666;