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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723403	XR_001748160.2	n.1562G>A		non_coding_transcript_exon_variant	Exon 2 of 3
LOC102723403	XR_001748161.2	n.1491G>A		non_coding_transcript_exon_variant	Exon 2 of 3
LOC102723403	XR_001748162.1	n.1491G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;