ENST00000544925.1:n.50+12542T>C

Variant names:

• chr11-114343980-A-G
• rs2852438
• ENST00000544925.1:n.50+12542T>C

Variant summary

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

The ENST00000544925.1(ENSG00000256947):​n.50+12542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 151,846 control chromosomes in the GnomAD database, including 749 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 0.096 (749 hom., cov: 31)
• Consequence: ENSG00000256947 ENST00000544925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

ENSG00000256947 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 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
ENSG00000256947	ENST00000544925.1	n.50+12542T>C		intron_variant	Intron 1 of 2	5
ENSG00000256195	ENST00000658199.1	n.492-616T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14563 AN: 151728 Hom.: 752 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0940

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0960 AC: 14570 AN: 151846 Hom.: 749 Cov.: 31 AF XY: 0.0934 AC XY: 6930 AN XY: 74186

African (AFR) AF: 0.124 AC: 5119 AN: 41362

American (AMR) AF: 0.0649 AC: 989 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3466

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0779 AC: 375 AN: 4814

European-Finnish (FIN) AF: 0.0799 AC: 841 AN: 10522

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6387 AN: 67968

Other (OTH) AF: 0.0905 AC: 191 AN: 2110

Alfa AF: 0.0961 Hom.: 1386

Bravo AF: 0.0963

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.54
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2852438; hg19: chr11-114214702;