ENST00000731302.1:n.459-7808A>G

Variant names:

• chr7-37522765-A-G
• rs1425132
• ENST00000731302.1:n.459-7808A>G

Variant summary

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

The ENST00000731302.1(ENSG00000295610):​n.459-7808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,068 control chromosomes in the GnomAD database, including 14,174 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 0.43 (14174 hom., cov: 32)
• Consequence: ENSG00000295610 ENST00000731302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 5 publications found

Genes affected

ENSG00000295610 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295610	ENST00000731302.1	n.459-7808A>G		intron_variant	Intron 1 of 2
ENSG00000295610	ENST00000731303.1	n.459-24081A>G		intron_variant	Intron 1 of 2
ENSG00000295610	ENST00000731304.1	n.63-7808A>G		intron_variant	Intron 1 of 3
ENSG00000295610	ENST00000731305.1	n.462-7808A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64973 AN: 151950 Hom.: 14167 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.428 AC: 65011 AN: 152068 Hom.: 14174 Cov.: 32 AF XY: 0.425 AC XY: 31621 AN XY: 74330

African (AFR) AF: 0.353 AC: 14646 AN: 41480

American (AMR) AF: 0.420 AC: 6419 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3466

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5164

South Asian (SAS) AF: 0.410 AC: 1976 AN: 4822

European-Finnish (FIN) AF: 0.447 AC: 4729 AN: 10584

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32550 AN: 67970

Other (OTH) AF: 0.452 AC: 953 AN: 2108

Alfa AF: 0.462 Hom.: 67568

Bravo AF: 0.427

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1425132; hg19: chr7-37562368;