chr11-128399130-T-G

Variant names:

• chr11-128399130-T-G
• rs2323123
• ENST00000743958.1:n.87-25110A>C

Variant summary

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

The ENST00000743958.1(ENSG00000296974):​n.87-25110A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,202 control chromosomes in the GnomAD database, including 30,558 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 0.60 (30558 hom., cov: 32)
• Consequence: ENSG00000296974 ENST00000743958.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 3 publications found

Genes affected

ENSG00000296974 (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 (AFR) allele frequency at 95% confidence interval = 0.887 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
ENSG00000296974	ENST00000743958.1	n.87-25110A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91135 AN: 152084 Hom.: 30505 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.599 AC: 91238 AN: 152202 Hom.: 30558 Cov.: 32 AF XY: 0.596 AC XY: 44371 AN XY: 74408

African (AFR) AF: 0.895 AC: 37178 AN: 41562

American (AMR) AF: 0.481 AC: 7357 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3472

East Asian (EAS) AF: 0.882 AC: 4574 AN: 5184

South Asian (SAS) AF: 0.703 AC: 3396 AN: 4828

European-Finnish (FIN) AF: 0.360 AC: 3803 AN: 10560

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31266 AN: 67994

Other (OTH) AF: 0.570 AC: 1204 AN: 2112

Alfa AF: 0.339 Hom.: 793

Bravo AF: 0.617

Asia WGS AF: 0.772 AC: 2685 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	1.8
DANN	Benign	0.85
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2323123; hg19: chr11-128269025;