rs11123469

Variant names:

• chr2-118086607-T-C
• rs11123469
• ENST00000747807.1:n.1146A>G

Variant summary

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

The ENST00000747807.1(ENSG00000297418):​n.1146A>G 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 0.141 in 152,226 control chromosomes in the GnomAD database, including 1,834 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 (1834 hom., cov: 33)
• Consequence: ENSG00000297418 ENST00000747807.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 8 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+1644A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747807.1	n.1146A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297418	ENST00000747789.1	n.231+906A>G		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+1644A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21387 AN: 152108 Hom.: 1834 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.141 AC: 21397 AN: 152226 Hom.: 1834 Cov.: 33 AF XY: 0.140 AC XY: 10394 AN XY: 74408

African (AFR) AF: 0.204 AC: 8472 AN: 41532

American (AMR) AF: 0.193 AC: 2945 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1704 AN: 5176

South Asian (SAS) AF: 0.135 AC: 649 AN: 4824

European-Finnish (FIN) AF: 0.0822 AC: 872 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5989 AN: 68006

Other (OTH) AF: 0.122 AC: 259 AN: 2116

Alfa AF: 0.122 Hom.: 2465

Bravo AF: 0.156

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0050
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11123469; hg19: chr2-118844183;