11-88360542-T-C

Variant names:

• chr11-88360542-T-C
• rs4753359
• ENST00000684900.2:n.213-12695T>C

Variant summary

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

The NR_188508.1(LOC101929174):​n.174-12695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,974 control chromosomes in the GnomAD database, including 14,986 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 0.43 (14986 hom., cov: 31)
• Consequence: LOC101929174 NR_188508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 9 publications found

Genes affected

ENSG00000288018 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188508.1. 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
	LOC101929174	NR_188508.1		n.174-12695T>C		intron	N/A
	LOC101929174	NR_188509.1		n.174-12695T>C		intron	N/A
	LOC101929174	NR_188510.1		n.174-12695T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288018	ENST00000684900.2		n.213-12695T>C		intron	N/A
	ENSG00000288018	ENST00000689290.2		n.240-12695T>C		intron	N/A
	ENSG00000288018	ENST00000690686.2		n.228-12695T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64954 AN: 151856 Hom.: 14969 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.428 AC: 65016 AN: 151974 Hom.: 14986 Cov.: 31 AF XY: 0.440 AC XY: 32691 AN XY: 74278

African (AFR) AF: 0.549 AC: 22734 AN: 41426

American (AMR) AF: 0.489 AC: 7473 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3465 AN: 5172

South Asian (SAS) AF: 0.656 AC: 3157 AN: 4816

European-Finnish (FIN) AF: 0.403 AC: 4251 AN: 10548

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21491 AN: 67948

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.359 Hom.: 32884

Bravo AF: 0.437

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.63
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4753359; hg19: chr11-88093710;