rs12115114

Variant names:

• chr8-63477322-A-G
• rs12115114
• ENST00000655858.1:n.442A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-63477322-A-G
• chr8-63477322-A-T

Variant summary

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

The ENST00000655858.1(ENSG00000253894):​n.442A>G 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 0.874 in 152,190 control chromosomes in the GnomAD database, including 58,471 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 0.87 (58471 hom., cov: 31)
• Consequence: ENSG00000253894 ENST00000655858.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 8 publications found

Genes affected

ENSG00000253894 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655858.1. 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
	ENSG00000253894	ENST00000655858.1		n.442A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000253894	ENST00000740903.1		n.482+22A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132963 AN: 152072 Hom.: 58410 Cov.: 31

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.874 AC: 133083 AN: 152190 Hom.: 58471 Cov.: 31 AF XY: 0.876 AC XY: 65138 AN XY: 74376

African (AFR) AF: 0.968 AC: 40223 AN: 41562

American (AMR) AF: 0.898 AC: 13726 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2745 AN: 3472

East Asian (EAS) AF: 0.951 AC: 4907 AN: 5158

South Asian (SAS) AF: 0.937 AC: 4526 AN: 4828

European-Finnish (FIN) AF: 0.800 AC: 8462 AN: 10576

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.819 AC: 55706 AN: 68000

Other (OTH) AF: 0.873 AC: 1846 AN: 2114

Alfa AF: 0.839 Hom.: 94380

Bravo AF: 0.885

Asia WGS AF: 0.939 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		0.043

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: rs12115114;

hg19: chr8-64389880;