18-3328748-T-C

Variant names:

• chr18-3328748-T-C
• rs1623523
• ENST00000578787.2:n.1035+1310T>C

Variant summary

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

The ENST00000578787.2(ENSG00000266578):​n.1035+1310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,206 control chromosomes in the GnomAD database, including 3,288 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 0.21 (3288 hom., cov: 32)
• Consequence: ENSG00000266578 ENST00000578787.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

ENSG00000266578 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 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
ENSG00000266578	ENST00000578787.2	n.1035+1310T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31204 AN: 152088 Hom.: 3281 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.205 AC: 31236 AN: 152206 Hom.: 3288 Cov.: 32 AF XY: 0.204 AC XY: 15185 AN XY: 74406

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.205

Alfa AF: 0.220 Hom.: 3798

Bravo AF: 0.213

Asia WGS AF: 0.167 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1623523; hg19: chr18-3328746;