rs8091237

chr18-60385970-C-G

Variant summary

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

The ENST00000658928.1(ENSG00000285681):n.156+56625C>G 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 0.166 in 152,092 control chromosomes in the GnomAD database, including 2,546 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 0.17 (2546 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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 (NFE) allele frequency at 95% confidence interval = 0.225 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+56625C>G		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+56625C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25290 AN: 151974 Hom.: 2547 Cov.: 32

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.166 AC: 25285 AN: 152092 Hom.: 2546 Cov.: 32 AF XY: 0.163 AC XY: 12086 AN XY: 74334

Gnomad4 AFR AF: 0.0634

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.0968

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.174

Alfa AF: 0.187 Hom.: 375

Bravo AF: 0.162

Asia WGS AF: 0.137 AC: 476 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	0.066
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8091237; hg19: chr18-58053203;