rs10891549

Variant names:

• chr11-113407725-T-C
• rs10891549
• ENST00000546284.1:n.244+1758T>C

Variant summary

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

The ENST00000546284.1(ENSG00000256757):​n.244+1758T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,202 control chromosomes in the GnomAD database, including 13,868 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 0.39 (13868 hom., cov: 33)
• Consequence: ENSG00000256757 ENST00000546284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 17 publications found

Genes affected

ENSG00000256757 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 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
ENSG00000256757	ENST00000546284.1	n.244+1758T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59381 AN: 152084 Hom.: 13881 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.390 AC: 59362 AN: 152202 Hom.: 13868 Cov.: 33 AF XY: 0.382 AC XY: 28433 AN XY: 74414

African (AFR) AF: 0.175 AC: 7256 AN: 41542

American (AMR) AF: 0.333 AC: 5096 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5172

South Asian (SAS) AF: 0.353 AC: 1705 AN: 4824

European-Finnish (FIN) AF: 0.445 AC: 4713 AN: 10594

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36777 AN: 67988

Other (OTH) AF: 0.439 AC: 929 AN: 2114

Alfa AF: 0.489 Hom.: 51533

Bravo AF: 0.374

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.69
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10891549; hg19: chr11-113278447;