18-60130586-A-G

Position:

• chr18-60130586-A-G

Variant summary

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

The ENST00000588794.1(ENSG00000267686):​n.346+931A>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 0.0651 in 152,238 control chromosomes in the GnomAD database, including 427 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 0.065 (427 hom., cov: 32)
• Consequence: ENST00000588794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

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 = 0.0912 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
	ENST00000588794.1	n.346+931A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000668793.1	n.240+931A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9913 AN: 152120 Hom.: 428 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0651 AC: 9908 AN: 152238 Hom.: 427 Cov.: 32 AF XY: 0.0622 AC XY: 4633 AN XY: 74436

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0806 Hom.: 318

Bravo AF: 0.0669

Asia WGS AF: 0.0140 AC: 48 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	1.1
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: rs17772748; hg19: chr18-57797818;