11-46158303-C-T

Variant names:

• chr11-46158303-C-T
• rs2029483
• ENST00000635144.1:n.343-16282C>T

Variant summary

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

The ENST00000635144.1(ENSG00000255314):​n.343-16282C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,172 control chromosomes in the GnomAD database, including 62,514 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 0.90 (62514 hom., cov: 31)
• Consequence: ENSG00000255314 ENST00000635144.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 0 publications found

Genes affected

ENSG00000255314 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000255314	ENST00000635144.1	n.343-16282C>T		intron_variant	Intron 2 of 3	5
ENSG00000255314	ENST00000649677.1	n.282-16282C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137071 AN: 152054 Hom.: 62491 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.901 AC: 137143 AN: 152172 Hom.: 62514 Cov.: 31 AF XY: 0.904 AC XY: 67240 AN XY: 74392

African (AFR) AF: 0.747 AC: 30972 AN: 41466

American (AMR) AF: 0.951 AC: 14544 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3390 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5172 AN: 5176

South Asian (SAS) AF: 0.929 AC: 4482 AN: 4824

European-Finnish (FIN) AF: 0.972 AC: 10303 AN: 10604

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65257 AN: 68024

Other (OTH) AF: 0.921 AC: 1945 AN: 2112

Alfa AF: 0.943 Hom.: 71811

Bravo AF: 0.894

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.42
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs2029483; hg19: chr11-46179854;