rs627202

Variant names:

• chr18-2292492-C-A
• rs627202
• ENST00000639316.2:n.354+42578G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-2292492-C-A
• chr18-2292492-C-G
• chr18-2292492-C-T

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.354+42578G>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: ENSG00000263745 ENST00000639316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

ENSG00000263745 (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=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263745	ENST00000639316.2	n.354+42578G>T		intron_variant	Intron 2 of 4	5
ENSG00000263745	ENST00000746279.1	n.185+42578G>T		intron_variant	Intron 2 of 4
ENSG00000263745	ENST00000746280.1	n.96+34580G>T		intron_variant	Intron 1 of 5
ENSG00000263745	ENST00000746281.1	n.85+34580G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.30
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs627202; hg19: chr18-2292491;