1-7901146-C-T

Position:

• chr1-7901146-C-T

Variant summary

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

The XM_011540537.3(UTS2):​c.-75+12035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,084 control chromosomes in the GnomAD database, including 32,223 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 0.65 (32223 hom., cov: 33)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+12035G>A		intron_variant			XP_011538839.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98010 AN: 151966 Hom.: 32174 Cov.: 33

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.645 AC: 98118 AN: 152084 Hom.: 32223 Cov.: 33 AF XY: 0.645 AC XY: 47955 AN XY: 74312

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.626

Alfa AF: 0.589 Hom.: 43440

Bravo AF: 0.655

Asia WGS AF: 0.651 AC: 2262 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	1.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227163; hg19: chr1-7961206;