11-109022119-C-T

Variant names:

• chr11-109022119-C-T
• rs4754373
• ENST00000526041.2:n.283+15624G>A

Variant summary

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

The ENST00000526041.2(ENSG00000255528):​n.283+15624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,040 control chromosomes in the GnomAD database, including 3,611 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 0.21 (3611 hom., cov: 33)
• Consequence: ENSG00000255528 ENST00000526041.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 2 publications found

Genes affected

ENSG00000255528 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 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
ENSG00000255528	ENST00000526041.2	n.283+15624G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32005 AN: 151922 Hom.: 3604 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.211 AC: 32031 AN: 152040 Hom.: 3611 Cov.: 33 AF XY: 0.211 AC XY: 15688 AN XY: 74288

African (AFR) AF: 0.265 AC: 11016 AN: 41492

American (AMR) AF: 0.218 AC: 3330 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3464

East Asian (EAS) AF: 0.275 AC: 1421 AN: 5164

South Asian (SAS) AF: 0.153 AC: 737 AN: 4814

European-Finnish (FIN) AF: 0.205 AC: 2165 AN: 10552

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12208 AN: 67972

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.184 Hom.: 1452

Bravo AF: 0.218

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs4754373; hg19: chr11-108892846;