1-7867921-C-T

Position:

• chr1-7867921-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.-74-14416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,212 control chromosomes in the GnomAD database, including 60,982 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 0.89 (60982 hom., cov: 32)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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 (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-14416G>A		intron_variant			XP_011538839.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135945 AN: 152094 Hom.: 60928 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.894 AC: 136056 AN: 152212 Hom.: 60982 Cov.: 32 AF XY: 0.898 AC XY: 66793 AN XY: 74414

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.897

Alfa AF: 0.905 Hom.: 82777

Bravo AF: 0.888

Asia WGS AF: 0.933 AC: 3245 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	0.31
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs579992; hg19: chr1-7927981;