18-60657832-C-T

Variant names:

• chr18-60657832-C-T
• rs12962651
• ENST00000591869.1:n.229-7007G>A

Variant summary

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

The ENST00000591869.1(ENSG00000267098):​n.229-7007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,852 control chromosomes in the GnomAD database, including 15,677 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 0.44 (15677 hom., cov: 32)
• Consequence: ENSG00000267098 ENST00000591869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

Genes affected

ENSG00000267098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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
ENSG00000267098	ENST00000591869.1	n.229-7007G>A		intron_variant	Intron 5 of 7	4
ENSG00000267098	ENST00000655645.1	n.165-7007G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66343 AN: 151736 Hom.: 15671 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.437 AC: 66353 AN: 151852 Hom.: 15677 Cov.: 32 AF XY: 0.440 AC XY: 32696 AN XY: 74232

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.473

Alfa AF: 0.458 Hom.: 2779

Bravo AF: 0.419

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
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: rs12962651; hg19: chr18-58325065;