rs934078

chr12-114622198-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000547819.1(ENSG00000258254):n.251+187G>A variant causes a intron, non coding transcript 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: ENST00000547819.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903026	XR_007063470.1	n.615+187G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000547819.1	n.251+187G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0747

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.0950

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.109

Alfa AF: 0.101 Hom.: 576

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934078; hg19: chr12-115060003;