chr18-24785204-G-A

Variant names:

• chr18-24785204-G-A
• rs6508329
• ENST00000577354.6:n.561+18470G>A

Variant summary

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

The ENST00000577354.6(ENSG00000266573):​n.561+18470G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,012 control chromosomes in the GnomAD database, including 2,690 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 0.17 (2690 hom., cov: 32)
• Consequence: ENSG00000266573 ENST00000577354.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• Publications: 3 publications found

Genes affected

ENSG00000266573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577354.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266573	ENST00000577354.6	TSL:4	n.561+18470G>A		intron	N/A
	ENSG00000266573	ENST00000582650.5	TSL:4	n.235+58447G>A		intron	N/A
	ENSG00000266573	ENST00000654065.1		n.226+58447G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25823 AN: 151894 Hom.: 2693 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.170 AC: 25818 AN: 152012 Hom.: 2690 Cov.: 32 AF XY: 0.173 AC XY: 12835 AN XY: 74270

African (AFR) AF: 0.0469 AC: 1948 AN: 41520

American (AMR) AF: 0.164 AC: 2509 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1216 AN: 5134

South Asian (SAS) AF: 0.236 AC: 1132 AN: 4798

European-Finnish (FIN) AF: 0.244 AC: 2573 AN: 10556

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14918 AN: 67954

Other (OTH) AF: 0.211 AC: 444 AN: 2104

Alfa AF: 0.112 Hom.: 244

Bravo AF: 0.159

Asia WGS AF: 0.226 AC: 784 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.72
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6508329; hg19: chr18-22365168;