18-2483515-A-G

Variant names:

• chr18-2483515-A-G
• rs7230412
• ENST00000639316.2:n.268+5644T>C

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.268+5644T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,972 control chromosomes in the GnomAD database, including 8,628 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 0.33 (8628 hom., cov: 32)
• Consequence: ENSG00000263745 ENST00000639316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 1 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639316.2. 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
	ENSG00000263745	ENST00000639316.2	TSL:5	n.268+5644T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50472 AN: 151854 Hom.: 8613 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.332 AC: 50522 AN: 151972 Hom.: 8628 Cov.: 32 AF XY: 0.338 AC XY: 25128 AN XY: 74262

African (AFR) AF: 0.252 AC: 10453 AN: 41440

American (AMR) AF: 0.430 AC: 6571 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3464

East Asian (EAS) AF: 0.278 AC: 1440 AN: 5172

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4818

European-Finnish (FIN) AF: 0.440 AC: 4637 AN: 10536

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22989 AN: 67954

Other (OTH) AF: 0.325 AC: 687 AN: 2116

Alfa AF: 0.338 Hom.: 28315

Bravo AF: 0.332

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.70
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7230412; hg19: chr18-2483514;