rs11044889

Positions:

• chr12-19823208-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000535764.1(ENSG00000255910):​n.153+47605T>C variant causes a intron, non coding transcript 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: ENST00000535764.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000535764.1	n.153+47605T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.272

Alfa AF: 0.287 Hom.: 1060

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11044889; hg19: chr12-19976142;