rs2296590

Positions:

• chr10-102502871-G-A

Variant summary

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

The XM_047425335.1(SUFU):​c.-145G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,118 control chromosomes in the GnomAD database, including 9,539 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 0.35 (9539 hom., cov: 33)
• Consequence: SUFU XM_047425335.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

SUFU (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUFU	XM_011539863.4	c.-108G>A		5_prime_UTR_variant	1/13		XP_011538165.1
SUFU	XM_047425335.1	c.-145G>A		5_prime_UTR_variant	1/14		XP_047281291.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53376 AN: 152000 Hom.: 9527 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.351 AC: 53411 AN: 152118 Hom.: 9539 Cov.: 33 AF XY: 0.352 AC XY: 26199 AN XY: 74372

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.310

Alfa AF: 0.336 Hom.: 14777

Bravo AF: 0.354

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296590; hg19: chr10-104262628;