rs1496483

Variant names:

• chr18-28677558-T-G
• rs1496483
• ENST00000649159.1:n.65+38780T>G

Variant summary

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

The ENST00000649159.1(ENSG00000265994):​n.65+38780T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,974 control chromosomes in the GnomAD database, including 4,925 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 0.25 (4925 hom., cov: 32)
• Consequence: ENSG00000265994 ENST00000649159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

Genes affected

ENSG00000265994 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 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
ENSG00000265994	ENST00000649159.1	n.65+38780T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37829 AN: 151856 Hom.: 4922 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.249 AC: 37842 AN: 151974 Hom.: 4925 Cov.: 32 AF XY: 0.249 AC XY: 18519 AN XY: 74276

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.219

Alfa AF: 0.266 Hom.: 930

Bravo AF: 0.241

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1496483; hg19: chr18-26257522;