rs11044889

Variant names:

• chr12-19823208-T-C
• rs11044889
• ENST00000535764.1:n.153+47605T>C

Variant summary

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

The ENST00000535764.1(ENSG00000255910):​n.153+47605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,794 control chromosomes in the GnomAD database, including 6,809 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 0.27 (6809 hom., cov: 32)
• Consequence: ENSG00000255910 ENST00000535764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 0 publications found

Genes affected

ENSG00000255910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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
ENSG00000255910	ENST00000535764.1	n.153+47605T>C		intron_variant	Intron 1 of 4	3
ENSG00000255910	ENST00000716354.1	n.256+47605T>C		intron_variant	Intron 1 of 10
ENSG00000255910	ENST00000716355.1	n.186+47605T>C		intron_variant	Intron 1 of 12

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41475 AN: 151676 Hom.: 6804 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.273 AC: 41500 AN: 151794 Hom.: 6809 Cov.: 32 AF XY: 0.268 AC XY: 19906 AN XY: 74164

African (AFR) AF: 0.105 AC: 4360 AN: 41378

American (AMR) AF: 0.312 AC: 4746 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.0973 AC: 500 AN: 5140

South Asian (SAS) AF: 0.146 AC: 696 AN: 4782

European-Finnish (FIN) AF: 0.377 AC: 3962 AN: 10520

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25198 AN: 67956

Other (OTH) AF: 0.272 AC: 575 AN: 2112

Alfa AF: 0.281 Hom.: 1063

Bravo AF: 0.264

Asia WGS AF: 0.126 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.74
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs11044889; hg19: chr12-19976142;