18-14294025-G-T

Variant names:

• chr18-14294025-G-T
• rs11664559
• ENST00000577614.2:n.1897+43618G>T

Variant summary

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

The ENST00000577614.2(ENSG00000283294):​n.1897+43618G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 144,030 control chromosomes in the GnomAD database, including 2,825 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 0.12 (2825 hom., cov: 28)
• Consequence: ENSG00000283294 ENST00000577614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

ENSG00000283294 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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
ENSG00000283294	ENST00000577614.2	n.1897+43618G>T		intron_variant	Intron 9 of 12	5

Frequencies

GnomAD3 genomes AF: 0.121 AC: 17426 AN: 143912 Hom.: 2824 Cov.: 28

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.116

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.121 AC: 17446 AN: 144030 Hom.: 2825 Cov.: 28 AF XY: 0.119 AC XY: 8341 AN XY: 70146

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.0612

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.0846

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0333 Hom.: 107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11664559; hg19: chr18-14294024;