11-88360542-T-C

Variant names:

• chr11-88360542-T-C
• rs4753359
• ENST00000684900.1:n.170-12695T>C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000288018 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929174	NR_188508.1	n.174-12695T>C		intron_variant	Intron 1 of 5
LOC101929174	NR_188509.1	n.174-12695T>C		intron_variant	Intron 1 of 3
LOC101929174	NR_188510.1	n.174-12695T>C		intron_variant	Intron 1 of 4
LOC101929174	NR_188511.1	n.174-12695T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288018	ENST00000684900.1	n.170-12695T>C		intron_variant	Intron 1 of 4
ENSG00000288018	ENST00000689290.1	n.207-12695T>C		intron_variant	Intron 1 of 3
ENSG00000288018	ENST00000690686.1	n.206-12695T>C		intron_variant	Intron 1 of 4
ENSG00000288018	ENST00000701412.1	n.219-12695T>C		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.401

Alfa AF: 0.342 Hom.: 19409

Bravo AF: 0.437

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4753359; hg19: chr11-88093710;