rs11873305

Positions:

• chr18-60381959-A-C

Variant summary

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

The ENST00000658928.1(ENSG00000285681):​n.156+52614A>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 0.11 in 152,162 control chromosomes in the GnomAD database, including 1,979 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 (1979 hom., cov: 31)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658928.1	n.156+52614A>C		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+52614A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16693 AN: 152044 Hom.: 1963 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.110 AC: 16744 AN: 152162 Hom.: 1979 Cov.: 31 AF XY: 0.106 AC XY: 7922 AN XY: 74412

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.0490

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0347

Gnomad4 FIN AF: 0.0282

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0504 Hom.: 470

Bravo AF: 0.121

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11873305; hg19: chr18-58049192;