rs2032366

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-61599138-C-A
• chr18-61599138-C-G
• chr18-61599138-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000587754.1(ENSG00000267175):​n.500+9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: ENSG00000267175 ENST00000587754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 0 publications found

Genes affected

ENSG00000267175 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904314	XR_007066394.1	n.1814+5798G>T		intron_variant	Intron 2 of 5
LOC124904314	XR_007066395.1	n.460+5798G>T		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>T		intron_variant	Intron 3 of 4	5
ENSG00000267175	ENST00000590199.6	n.622-6515G>T		intron_variant	Intron 3 of 3	3
ENSG00000267175	ENST00000590968.1	n.318-6515G>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.24
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;