rs2148843

Variant names:

• chr9-36779562-G-A
• rs2148843
• ENST00000670495.1:n.88G>A

Variant summary

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

The ENST00000670495.1(ENSG00000287514):​n.88G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 151,686 control chromosomes in the GnomAD database, including 1,373 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 0.078 (1373 hom., cov: 32)
• Consequence: ENSG00000287514 ENST00000670495.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 1 publications found

Genes affected

ENSG00000287514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670495.1. 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
	ENSG00000287514	ENST00000670495.1		n.88G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000287514	ENST00000658385.1		n.-79G>A		upstream_gene	N/A
	ENSG00000287514	ENST00000669987.2		n.-216G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11742 AN: 151568 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00907

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0000948

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00233

Gnomad OTH AF: 0.0610

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

GnomAD4 genome AF: 0.0776 AC: 11776 AN: 151686 Hom.: 1373 Cov.: 32 AF XY: 0.0752 AC XY: 5578 AN XY: 74174

African (AFR) AF: 0.253 AC: 10436 AN: 41254

American (AMR) AF: 0.0343 AC: 523 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3468

East Asian (EAS) AF: 0.00909 AC: 47 AN: 5170

South Asian (SAS) AF: 0.0881 AC: 421 AN: 4780

European-Finnish (FIN) AF: 0.0000948 AC: 1 AN: 10546

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00231 AC: 157 AN: 67936

Other (OTH) AF: 0.0604 AC: 127 AN: 2104

Alfa AF: 0.0322 Hom.: 322

Bravo AF: 0.0863

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2148843;

hg19: chr9-36779559;