ENST00000578787.3:n.1202+1310T>C

Variant names:

• chr18-3328748-T-C
• rs1623523
• ENST00000578787.3:n.1202+1310T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000578787.3(ENSG00000266578):​n.1202+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 ENST00000578787.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 5 publications found

Genes affected

ENSG00000266578 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578787.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266578	ENST00000578787.3	TSL:3	n.1202+1310T>C		intron	N/A
	ENSG00000301728	ENST00000781104.1		n.61+1878A>G		intron	N/A
	ENSG00000301728	ENST00000781105.1		n.114+1878A>G		intron	N/A

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

African (AFR) AF: 0.179 AC: 7453 AN: 41534

American (AMR) AF: 0.248 AC: 3790 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.162 AC: 842 AN: 5186

South Asian (SAS) AF: 0.202 AC: 974 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1982 AN: 10592

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14792 AN: 67996

Other (OTH) AF: 0.205 AC: 433 AN: 2116

Alfa AF: 0.217 Hom.: 5672

Bravo AF: 0.213

Asia WGS AF: 0.167 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1623523; hg19: chr18-3328746;