rs11114818

Variant names:

• chr12-76642272-T-G
• rs11114818
• ENST00000832799.1:n.554+9216T>G

Variant summary

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

The ENST00000832799.1(ENSG00000257526):​n.554+9216T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,260 control chromosomes in the GnomAD database, including 1,236 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 0.11 (1236 hom., cov: 32)
• Consequence: ENSG00000257526 ENST00000832799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 2 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369851	XR_945115.3	n.172-5623A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257526	ENST00000832799.1	n.554+9216T>G		intron_variant	Intron 3 of 5
ENSG00000257526	ENST00000832800.1	n.564+9216T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16325 AN: 152142 Hom.: 1232 Cov.: 32

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.107 AC: 16340 AN: 152260 Hom.: 1236 Cov.: 32 AF XY: 0.113 AC XY: 8377 AN XY: 74446

African (AFR) AF: 0.0318 AC: 1321 AN: 41572

American (AMR) AF: 0.115 AC: 1759 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3466

East Asian (EAS) AF: 0.361 AC: 1869 AN: 5184

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4826

European-Finnish (FIN) AF: 0.155 AC: 1641 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7968 AN: 68012

Other (OTH) AF: 0.119 AC: 251 AN: 2112

Alfa AF: 0.106 Hom.: 113

Bravo AF: 0.0985

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs11114818; hg19: chr12-77036052;