rs1490388

Variant names:

• chr6-126514509-C-A
• rs1490388
• ENST00000650727.1:n.3037-16984G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-126514509-C-A
• chr6-126514509-C-G
• chr6-126514509-C-T

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​n.3037-16984G>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: 32)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 43 publications found

Genes affected

ENSG00000293110 (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=-0.91).

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
ENSG00000293110	ENST00000650727.1	n.3037-16984G>T		intron_variant	Intron 14 of 14
ENSG00000293110	ENST00000651326.1	n.2290-41915G>T		intron_variant	Intron 5 of 6
ENSG00000293110	ENST00000652383.1	n.630+17154G>T		intron_variant	Intron 3 of 4
ENSG00000293110	ENST00000652545.1	n.3347-16984G>T		intron_variant	Intron 15 of 15

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.31
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1490388; hg19: chr6-126835655;