8-17806047-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000788923.1(ENSG00000302690):​n.105T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,030 control chromosomes in the GnomAD database, including 34,665 homozygotes. 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: 𝑓 0.64 (34665 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

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>G		intron	N/A
	MTUS1-DT	NR_186404.1		n.1387+2181A>G		intron	N/A
	MTUS1-DT	NR_186406.1		n.400-2895A>G		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96967 AN: 151910 Hom.: 34666 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.638 AC: 96976 AN: 152030 Hom.: 34665 Cov.: 32 AF XY: 0.633 AC XY: 47001 AN XY: 74294

African (AFR) AF: 0.316 AC: 13083 AN: 41444

American (AMR) AF: 0.653 AC: 9982 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2390 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2292 AN: 5160

South Asian (SAS) AF: 0.517 AC: 2492 AN: 4824

European-Finnish (FIN) AF: 0.823 AC: 8701 AN: 10576

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55621 AN: 67960

Other (OTH) AF: 0.688 AC: 1454 AN: 2114

Alfa AF: 0.719 Hom.: 16544

Bravo AF: 0.614

Asia WGS AF: 0.495 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.7
DANN	Benign	0.72
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;