11-125865825-C-G

Variant names:

• chr11-125865825-C-G
• rs2321469
• ENST00000751925.1:n.276+21362G>C

Variant summary

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

The ENST00000751925.1(ENSG00000297941):​n.276+21362G>C variant causes a intron change. The variant allele was found at a frequency of 0.84 in 151,704 control chromosomes in the GnomAD database, including 53,942 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 0.84 (53942 hom., cov: 28)
• Consequence: ENSG00000297941 ENST00000751925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

Genes affected

ENSG00000297941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000297941	ENST00000751925.1	n.276+21362G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127249 AN: 151588 Hom.: 53891 Cov.: 28

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.840 AC: 127357 AN: 151704 Hom.: 53942 Cov.: 28 AF XY: 0.841 AC XY: 62282 AN XY: 74084

African (AFR) AF: 0.717 AC: 29618 AN: 41302

American (AMR) AF: 0.899 AC: 13687 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3101 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5144 AN: 5156

South Asian (SAS) AF: 0.897 AC: 4304 AN: 4800

European-Finnish (FIN) AF: 0.856 AC: 8984 AN: 10498

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59824 AN: 67952

Other (OTH) AF: 0.840 AC: 1765 AN: 2102

Alfa AF: 0.845 Hom.: 2605

Bravo AF: 0.837

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.44

Splicing

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

Other links and lift over

dbSNP: rs2321469; hg19: chr11-125735720;