18-28463039-A-C

Variant names:

• chr18-28463039-A-C
• rs12966353
• ENST00000767551.1:n.395+4088A>C

Variant summary

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

The ENST00000767551.1(ENSG00000299932):​n.395+4088A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,032 control chromosomes in the GnomAD database, including 24,925 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 0.54 (24925 hom., cov: 32)
• Consequence: ENSG00000299932 ENST00000767551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 1 publications found

Genes affected

ENSG00000299932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767551.1. 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
	ENSG00000299932	ENST00000767551.1		n.395+4088A>C		intron	N/A
	ENSG00000299932	ENST00000767552.1		n.734+16644A>C		intron	N/A
	ENSG00000299932	ENST00000767553.1		n.278+16652A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81855 AN: 151914 Hom.: 24912 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.539 AC: 81889 AN: 152032 Hom.: 24925 Cov.: 32 AF XY: 0.544 AC XY: 40417 AN XY: 74272

African (AFR) AF: 0.231 AC: 9605 AN: 41494

American (AMR) AF: 0.653 AC: 9965 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2388 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4221 AN: 5172

South Asian (SAS) AF: 0.611 AC: 2947 AN: 4822

European-Finnish (FIN) AF: 0.636 AC: 6701 AN: 10534

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 44007 AN: 67970

Other (OTH) AF: 0.585 AC: 1235 AN: 2112

Alfa AF: 0.629 Hom.: 25918

Bravo AF: 0.530

Asia WGS AF: 0.683 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12966353; hg19: chr18-26043003;