rs11878133

chr18-60399804-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658928.1(ENSG00000285681):n.156+70459T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0439 in 152,264 control chromosomes in the GnomAD database, including 202 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 0.044 (202 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658928.1	n.156+70459T>C		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+70459T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0440 AC: 6690 AN: 152146 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0439 AC: 6689 AN: 152264 Hom.: 202 Cov.: 32 AF XY: 0.0428 AC XY: 3189 AN XY: 74456

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.0365

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0312 Hom.: 124

Bravo AF: 0.0482

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11878133; hg19: chr18-58067037;