rs289847

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000236885 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447078.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236885	ENST00000447078.1	TSL:4	n.90+16749G>T		intron	N/A
	ENSG00000236885	ENST00000652733.1		n.69+16749G>T		intron	N/A
	ENSG00000305708	ENST00000812528.1		n.142+5183G>T		intron	N/A

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

African (AFR) AF: 0.801 AC: 33254 AN: 41494

American (AMR) AF: 0.442 AC: 6732 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2061 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2409 AN: 5160

South Asian (SAS) AF: 0.676 AC: 3256 AN: 4820

European-Finnish (FIN) AF: 0.399 AC: 4202 AN: 10544

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34144 AN: 67924

Other (OTH) AF: 0.589 AC: 1243 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.42
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs289847; hg19: chr2-152025885;