rs12294104

Variant names:

• chr11-30361352-C-T
• rs12294104
• XR_001748160.2:n.1562G>A

Variant summary

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

The XR_001748160.2(LOC102723403):​n.1562G>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 0.136 in 152,054 control chromosomes in the GnomAD database, including 1,450 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 0.14 (1450 hom., cov: 32)
• Consequence: LOC102723403 XR_001748160.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 32 publications found

Genes affected

LOC102723403 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20722 AN: 151936 Hom.: 1448 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.136 AC: 20725 AN: 152054 Hom.: 1450 Cov.: 32 AF XY: 0.135 AC XY: 10065 AN XY: 74304

African (AFR) AF: 0.0913 AC: 3788 AN: 41498

American (AMR) AF: 0.136 AC: 2083 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.0884 AC: 456 AN: 5158

South Asian (SAS) AF: 0.105 AC: 506 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1846 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11132 AN: 67954

Other (OTH) AF: 0.131 AC: 276 AN: 2110

Alfa AF: 0.157 Hom.: 6083

Bravo AF: 0.132

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12294104; hg19: chr11-30382899;