chr1-7854117-G-A

Position:

• chr1-7854117-G-A

Variant summary

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

The XM_011540537.3(UTS2):​c.-74-612C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,480 control chromosomes in the GnomAD database, including 20,432 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 0.51 (20432 hom., cov: 30)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-612C>T		intron_variant			XP_011538839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77660 AN: 151362 Hom.: 20421 Cov.: 30

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.513 AC: 77699 AN: 151480 Hom.: 20432 Cov.: 30 AF XY: 0.508 AC XY: 37620 AN XY: 74028

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.548

Alfa AF: 0.387 Hom.: 1027

Bravo AF: 0.501

Asia WGS AF: 0.496 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228647; hg19: chr1-7914177; COSMIC: COSV50013200;