ENST00000541135.5:c.378-15018A>G

Variant names:

• chr11-61453646-A-G
• rs729404
• ENST00000541135.5:c.378-15018A>G

Variant summary

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

The ENST00000541135.5(ENSG00000256591):​c.378-15018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,218 control chromosomes in the GnomAD database, including 43,461 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 0.72 (43461 hom., cov: 33)
• Consequence: ENSG00000256591 ENST00000541135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 5 publications found

Genes affected

ENSG00000256591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 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
ENSG00000256591	ENST00000541135.5	c.378-15018A>G		intron_variant	Intron 3 of 4	4		ENSP00000443130.1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109917 AN: 152100 Hom.: 43464 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.722 AC: 109926 AN: 152218 Hom.: 43461 Cov.: 33 AF XY: 0.729 AC XY: 54277 AN XY: 74448

African (AFR) AF: 0.367 AC: 15250 AN: 41498

American (AMR) AF: 0.825 AC: 12630 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3094 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5035 AN: 5188

South Asian (SAS) AF: 0.820 AC: 3963 AN: 4832

European-Finnish (FIN) AF: 0.884 AC: 9368 AN: 10602

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57886 AN: 68008

Other (OTH) AF: 0.765 AC: 1616 AN: 2112

Alfa AF: 0.701 Hom.: 2963

Bravo AF: 0.703

Asia WGS AF: 0.822 AC: 2859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs729404; hg19: chr11-61221118;