18-24526812-C-T

Position:

• chr18-24526812-C-T

Variant summary

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

The ENST00000668994.1(ENSG00000266489):​n.357-8724G>A 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 0.459 in 151,698 control chromosomes in the GnomAD database, including 16,788 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 0.46 (16788 hom., cov: 31)
• Consequence: ENST00000668994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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
	ENST00000668994.1	n.357-8724G>A		intron_variant, non_coding_transcript_variant
	ENST00000581648.2	n.1311-8724G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000662616.1	n.367-5441G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69566 AN: 151580 Hom.: 16768 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.459 AC: 69633 AN: 151698 Hom.: 16788 Cov.: 31 AF XY: 0.460 AC XY: 34071 AN XY: 74108

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.453

Alfa AF: 0.393 Hom.: 24249

Bravo AF: 0.476

Asia WGS AF: 0.552 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7235440; hg19: chr18-22106776;