18-61599138-C-T

Variant names:

• chr18-61599138-C-T
• rs2032366
• ENST00000587754.1:n.500+9G>A

Variant summary

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

The ENST00000590968.1(ENSG00000267175):​n.318-6515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,854 control chromosomes in the GnomAD database, including 29,815 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 0.62 (29813 hom., cov: 30)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENSG00000267175 ENST00000590968.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 6 publications found

Genes affected

ENSG00000267175 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590968.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267175	ENST00000587754.1	TSL:5	n.500+9G>A		intron	N/A
	ENSG00000267175	ENST00000590199.6	TSL:3	n.622-6515G>A		intron	N/A
	ENSG00000267175	ENST00000590968.1	TSL:2	n.318-6515G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94726 AN: 151732 Hom.: 29787 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.624 AC: 94806 AN: 151850 Hom.: 29813 Cov.: 30 AF XY: 0.620 AC XY: 45965 AN XY: 74194

African (AFR) AF: 0.697 AC: 28821 AN: 41374

American (AMR) AF: 0.592 AC: 9037 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3466

East Asian (EAS) AF: 0.584 AC: 3007 AN: 5148

South Asian (SAS) AF: 0.499 AC: 2402 AN: 4810

European-Finnish (FIN) AF: 0.590 AC: 6214 AN: 10538

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.603 AC: 40954 AN: 67936

Other (OTH) AF: 0.642 AC: 1354 AN: 2110

Alfa AF: 0.607 Hom.: 117622

Bravo AF: 0.630

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.21
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2032366;

hg19: chr18-59266371;