18-24837937-A-G

Variant names:

• chr18-24837937-A-G
• rs10502459
• ENST00000577354.6:n.561+71203A>G

Variant summary

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

The ENST00000577354.6(ENSG00000266573):​n.561+71203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,192 control chromosomes in the GnomAD database, including 797 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 0.066 (797 hom., cov: 33)
• Consequence: ENSG00000266573 ENST00000577354.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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+71203A>G		intron	N/A
	ENSG00000266573	ENST00000582650.5	TSL:4	n.236-89901A>G		intron	N/A
	ENSG00000266573	ENST00000654065.1		n.227-98045A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10070 AN: 152074 Hom.: 798 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00366

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0663 AC: 10089 AN: 152192 Hom.: 797 Cov.: 33 AF XY: 0.0691 AC XY: 5142 AN XY: 74420

African (AFR) AF: 0.142 AC: 5902 AN: 41518

American (AMR) AF: 0.130 AC: 1994 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1140 AN: 5160

South Asian (SAS) AF: 0.104 AC: 502 AN: 4812

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10604

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00366 AC: 249 AN: 68010

Other (OTH) AF: 0.0581 AC: 123 AN: 2116

Alfa AF: 0.00881 Hom.: 3

Bravo AF: 0.0780

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.68
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10502459; hg19: chr18-22417901;