chr18-68315119-A-G

Variant names:

• chr18-68315119-A-G
• rs12458992
• ENST00000661028.1:n.318+12844T>C

Variant summary

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

The ENST00000661028.1(ENSG00000287907):​n.318+12844T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,156 control chromosomes in the GnomAD database, including 6,986 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 0.29 (6986 hom., cov: 29)
• Consequence: ENSG00000287907 ENST00000661028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

ENSG00000287907 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287907	ENST00000661028.1	n.318+12844T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44115 AN: 151036 Hom.: 6981 Cov.: 29

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.292 AC: 44123 AN: 151156 Hom.: 6986 Cov.: 29 AF XY: 0.292 AC XY: 21564 AN XY: 73808

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.322

Alfa AF: 0.197 Hom.: 438

Bravo AF: 0.284

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12458992; hg19: chr18-65982356;