ENST00000754158.1:n.324+8635A>G

Variant names:

• chr4-11131521-A-G
• rs4697674
• ENST00000754158.1:n.324+8635A>G

Variant summary

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

The ENST00000754158.1(ENSG00000298262):​n.324+8635A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,178 control chromosomes in the GnomAD database, including 358 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 0.063 (358 hom., cov: 32)
• Consequence: ENSG00000298262 ENST00000754158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 1 publications found

Genes affected

ENSG00000298262 (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 (NFE) allele frequency at 95% confidence interval = 0.0759 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
ENSG00000298262	ENST00000754158.1	n.324+8635A>G		intron_variant	Intron 4 of 5
ENSG00000298262	ENST00000754159.1	n.562+10690A>G		intron_variant	Intron 2 of 3
ENSG00000298262	ENST00000754160.1	n.487-30242A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9651 AN: 152062 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0383

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0634 AC: 9653 AN: 152178 Hom.: 358 Cov.: 32 AF XY: 0.0649 AC XY: 4829 AN XY: 74378

African (AFR) AF: 0.0382 AC: 1589 AN: 41554

American (AMR) AF: 0.0496 AC: 758 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0652 AC: 313 AN: 4804

European-Finnish (FIN) AF: 0.125 AC: 1320 AN: 10584

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0777 AC: 5280 AN: 67996

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0718 Hom.: 898

Bravo AF: 0.0556

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.53
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs4697674; hg19: chr4-11133145;