11-34812657-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.1044+58050T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309692	ENST00000843048.1	n.656+58050T>C		intron_variant	Intron 2 of 2
ENSG00000309692	ENST00000843049.1	n.848+58050T>C		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843050.1	n.440+58050T>C		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843051.1	n.298+58050T>C		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs12793173; hg19: chr11-34834204;