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 ENST00000587754.1(ENSG00000267175):​n.500+9G>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 ENST00000587754.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904314	XR_007066394.1	n.1814+5798G>A		intron_variant	Intron 2 of 5
LOC124904314	XR_007066395.1	n.460+5798G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267175	ENST00000587754.1	n.500+9G>A		intron_variant	Intron 3 of 4	5
ENSG00000267175	ENST00000590199.6	n.622-6515G>A		intron_variant	Intron 3 of 3	3
ENSG00000267175	ENST00000590968.1	n.318-6515G>A		intron_variant	Intron 3 of 3	2

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 v4.3

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

Other links and lift over

dbSNP: rs2032366; hg19: chr18-59266371;