rs4739140

Variant names:

• chr8-78840775-C-A
• rs4739140
• ENST00000649603.1:n.403+35080C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-78840775-C-A
• chr8-78840775-C-G
• chr8-78840775-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000649603.1(ENSG00000285744):​n.403+35080C>A 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: 33)
• Consequence: ENSG00000285744 ENST00000649603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

Genes affected

ENSG00000285744 (HGNC:56733): (metabolism induced tumor activator 1)

LINC02605 (HGNC:53974): (long intergenic non-protein coding RNA 2605)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MITA1	XR_001745965.2	n.1224+35080C>A		intron_variant	Intron 1 of 2
MITA1	XR_001745967.2	n.1225-10316C>A		intron_variant	Intron 1 of 3
MITA1	XR_001745970.2	n.1224+35080C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285744	ENST00000649603.1	n.403+35080C>A		intron_variant	Intron 1 of 5
LINC02605	ENST00000565297.2	n.*250C>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4739140; hg19: chr8-79753010;