8-17806047-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522768.1(MTUS1-DT):n.398+4305A>G variant causes a intron, non coding transcript 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: MTUS1-DT ENST00000522768.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS1-DT	ENST00000522768.1	n.398+4305A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.688

Alfa AF: 0.736 Hom.: 10139

Bravo AF: 0.614

Asia WGS AF: 0.495 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	7.7
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs471041; hg19: chr8-17663556;