ENST00000744088.1:n.160-569C>T

Variant names:

• chr11-76600576-G-A
• rs7124842
• ENST00000744088.1:n.160-569C>T

Variant summary

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

The ENST00000744088.1(ENSG00000296990):​n.160-569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,580 control chromosomes in the GnomAD database, including 1,043 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 0.11 (1043 hom., cov: 31)
• Consequence: ENSG00000296990 ENST00000744088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 5 publications found

Genes affected

ENSG00000296990 (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 (EAS) allele frequency at 95% confidence interval = 0.268 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
ENSG00000296990	ENST00000744088.1	n.160-569C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16630 AN: 151468 Hom.: 1040 Cov.: 31

Gnomad AFR AF: 0.0738

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.0756

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.110 AC: 16633 AN: 151580 Hom.: 1043 Cov.: 31 AF XY: 0.111 AC XY: 8226 AN XY: 74034

African (AFR) AF: 0.0738 AC: 3048 AN: 41316

American (AMR) AF: 0.0934 AC: 1422 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1438 AN: 5128

South Asian (SAS) AF: 0.0761 AC: 365 AN: 4798

European-Finnish (FIN) AF: 0.158 AC: 1650 AN: 10448

Middle Eastern (MID) AF: 0.0655 AC: 19 AN: 290

European-Non Finnish (NFE) AF: 0.119 AC: 8078 AN: 67894

Other (OTH) AF: 0.108 AC: 227 AN: 2106

Alfa AF: 0.114 Hom.: 2094

Bravo AF: 0.105

Asia WGS AF: 0.169 AC: 589 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	0.77
DANN	Benign	0.40
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7124842; hg19: chr11-76311620;