chr1-7884204-A-G

Position:

• chr1-7884204-A-G

Variant summary

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

The XM_011540537.3(UTS2):​c.-75+28977T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,028 control chromosomes in the GnomAD database, including 9,622 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 0.34 (9622 hom., cov: 32)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2	XM_011540537.3	c.-75+28977T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51970 AN: 151912 Hom.: 9626 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.342 AC: 51983 AN: 152028 Hom.: 9622 Cov.: 32 AF XY: 0.341 AC XY: 25321 AN XY: 74308

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.369

Alfa AF: 0.397 Hom.: 20922

Bravo AF: 0.332

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228703; hg19: chr1-7944264;