rs10891549

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000256757 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.439

Alfa AF: 0.521 Hom.: 34345

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10891549; hg19: chr11-113278447;