rs471041

Variant names:

• chr8-17806047-A-C
• rs471041
• ENST00000788923.1:n.105T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-17806047-A-C
• chr8-17806047-A-G

Variant summary

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

The ENST00000788923.1(ENSG00000302690):​n.105T>G variant causes a non coding transcript exon 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: ENSG00000302690 ENST00000788923.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 0 publications found

Genes affected

ENSG00000302690 (HGNC:):

MTUS1-DT (HGNC:55525): (MTUS1 divergent transcript)

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=-0.75).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788923.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS1-DT	NR_186403.1		n.402-3550A>C		intron	N/A
	MTUS1-DT	NR_186404.1		n.1387+2181A>C		intron	N/A
	MTUS1-DT	NR_186406.1		n.400-2895A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302690	ENST00000788923.1		n.105T>G		non_coding_transcript_exon	Exon 1 of 2
	MTUS1-DT	ENST00000522768.1	TSL:3	n.398+4305A>C		intron	N/A
	MTUS1-DT	ENST00000788486.1		n.290+2181A>C		intron	N/A

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.3
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs471041; hg19: chr8-17663556;