rs289847

Variant names:

• chr2-151169371-C-A
• rs289847
• ENST00000447078.1:n.90+16749G>T

Variant summary

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

The ENST00000447078.1(ENSG00000236885):​n.90+16749G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,972 control chromosomes in the GnomAD database, including 27,179 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 0.58 (27179 hom., cov: 32)
• Consequence: ENSG00000236885 ENST00000447078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

ENSG00000236885 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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
ENSG00000236885	ENST00000447078.1	n.90+16749G>T		intron_variant	Intron 1 of 2	4
ENSG00000236885	ENST00000652733.1	n.69+16749G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87847 AN: 151854 Hom.: 27122 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.579 AC: 87956 AN: 151972 Hom.: 27179 Cov.: 32 AF XY: 0.576 AC XY: 42740 AN XY: 74238

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.589

Alfa AF: 0.544 Hom.: 2864

Bravo AF: 0.586

Asia WGS AF: 0.594 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs289847; hg19: chr2-152025885;