rs8087522

chr18-60373245-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000658928.1(ENSG00000285681):n.156+43900G>A 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 0.379 in 151,896 control chromosomes in the GnomAD database, including 12,477 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.38 (12477 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 18-60373245-G-A is Benign according to our data. Variant chr18-60373245-G-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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+43900G>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+43900G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57467 AN: 151776 Hom.: 12442 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.379 AC: 57541 AN: 151896 Hom.: 12477 Cov.: 32 AF XY: 0.370 AC XY: 27464 AN XY: 74216

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.345

Alfa AF: 0.354 Hom.: 1875

Bravo AF: 0.397

Asia WGS AF: 0.235 AC: 816 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.36
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8087522; hg19: chr18-58040478;