7-25094230-T-C

Variant names:

• chr7-25094230-T-C
• rs39453
• ENST00000737690.1:n.51-15652T>C

Variant summary

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

The ENST00000737690.1(ENSG00000296268):​n.51-15652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,136 control chromosomes in the GnomAD database, including 8,619 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 0.33 (8619 hom., cov: 33)
• Consequence: ENSG00000296268 ENST00000737690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 15 publications found

Genes affected

ENSG00000296268 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737690.1. 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
	ENSG00000296268	ENST00000737690.1		n.51-15652T>C		intron	N/A
	ENSG00000296268	ENST00000737691.1		n.211+9117T>C		intron	N/A
	ENSG00000296268	ENST00000737692.1		n.52-15652T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50261 AN: 152018 Hom.: 8613 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.331 AC: 50288 AN: 152136 Hom.: 8619 Cov.: 33 AF XY: 0.334 AC XY: 24839 AN XY: 74372

African (AFR) AF: 0.247 AC: 10255 AN: 41530

American (AMR) AF: 0.340 AC: 5207 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1115 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1516 AN: 5176

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4810

European-Finnish (FIN) AF: 0.471 AC: 4979 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24765 AN: 67974

Other (OTH) AF: 0.328 AC: 692 AN: 2108

Alfa AF: 0.345 Hom.: 28196

Bravo AF: 0.318

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.42
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs39453; hg19: chr7-25133849;