rs934078

Variant names:

• chr12-114622198-G-A
• rs934078
• ENST00000547819.1:n.251+187G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-114622198-G-A
• chr12-114622198-G-C

Variant summary

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

The ENST00000547819.1(ENSG00000258254):​n.251+187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,120 control chromosomes in the GnomAD database, including 1,533 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 0.13 (1533 hom., cov: 33)
• Consequence: ENSG00000258254 ENST00000547819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 1 publications found

Genes affected

ENSG00000258254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547819.1. 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
	ENSG00000258254	ENST00000547819.1	TSL:3	n.251+187G>A		intron	N/A
	ENSG00000258254	ENST00000727028.1		n.504+187G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20133 AN: 152000 Hom.: 1529 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.133 AC: 20166 AN: 152120 Hom.: 1533 Cov.: 33 AF XY: 0.131 AC XY: 9760 AN XY: 74366

African (AFR) AF: 0.212 AC: 8798 AN: 41500

American (AMR) AF: 0.0747 AC: 1140 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5158

South Asian (SAS) AF: 0.0950 AC: 458 AN: 4820

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6746 AN: 68008

Other (OTH) AF: 0.109 AC: 229 AN: 2108

Alfa AF: 0.101 Hom.: 621

Bravo AF: 0.133

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.93
DANN	Benign	0.65
PhyloP100		-0.12

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: rs934078;

hg19: chr12-115060003;