rs12793173

Variant names:

• chr11-34812657-T-C
• rs12793173
• ENST00000843048.1:n.656+58050T>C

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.656+58050T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,970 control chromosomes in the GnomAD database, including 3,288 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 0.19 (3288 hom., cov: 32)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 23 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843048.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309692	ENST00000843048.1		n.656+58050T>C		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.848+58050T>C		intron	N/A
	ENSG00000309692	ENST00000843050.1		n.440+58050T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28503 AN: 151852 Hom.: 3286 Cov.: 32

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.188 AC: 28512 AN: 151970 Hom.: 3288 Cov.: 32 AF XY: 0.190 AC XY: 14122 AN XY: 74266

African (AFR) AF: 0.0593 AC: 2461 AN: 41466

American (AMR) AF: 0.167 AC: 2551 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3470

East Asian (EAS) AF: 0.121 AC: 627 AN: 5178

South Asian (SAS) AF: 0.331 AC: 1588 AN: 4804

European-Finnish (FIN) AF: 0.243 AC: 2560 AN: 10534

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16902 AN: 67934

Other (OTH) AF: 0.219 AC: 462 AN: 2110

Alfa AF: 0.233 Hom.: 15303

Bravo AF: 0.170

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.065
DANN	Benign	0.56
PhyloP100		-3.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12793173;

hg19: chr11-34834204;