18-1206983-C-T

Position:

• chr18-1206983-C-T

Variant summary

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

The ENST00000670380.1(ENSG00000263551):​n.732+23024C>T 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 0.791 in 152,028 control chromosomes in the GnomAD database, including 51,320 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 0.79 (51320 hom., cov: 32)
• Consequence: ENST00000670380.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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 = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371953	XR_001753318.2	n.885+9373C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670380.1	n.732+23024C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120179 AN: 151910 Hom.: 51310 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.791 AC: 120225 AN: 152028 Hom.: 51320 Cov.: 32 AF XY: 0.795 AC XY: 59088 AN XY: 74330

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.825

Alfa AF: 0.817 Hom.: 8902

Bravo AF: 0.770

Asia WGS AF: 0.826 AC: 2872 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	5.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1826508; hg19: chr18-1206984;