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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903026	XR_007063470.1	n.615+187G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258254	ENST00000547819.1	n.251+187G>A		intron_variant	Intron 1 of 1	3
ENSG00000258254	ENST00000727028.1	n.504+187G>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs934078; hg19: chr12-115060003;