rs10998112

chr10-68398295-T-C

Variant summary

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

The NM_001330103.2(RUFY2):c.297-1414A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,220 control chromosomes in the GnomAD database, including 373 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 0.060 (373 hom., cov: 32)
• Consequence: RUFY2 NM_001330103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806

Genes affected

RUFY2 (HGNC:19761): (RUN and FYVE domain containing 2) Enables SH3 domain binding activity. Predicted to be involved in regulation of endocytosis. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RUFY2	NM_001330103.2	c.297-1414A>G		intron_variant		ENST00000602465.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RUFY2	ENST00000602465.6	c.297-1414A>G		intron_variant		5	NM_001330103.2	P1

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9132 AN: 152102 Hom.: 371 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00910

Gnomad FIN AF: 0.0460

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0601 AC: 9144 AN: 152220 Hom.: 373 Cov.: 32 AF XY: 0.0583 AC XY: 4335 AN XY: 74412

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0374

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00890

Gnomad4 FIN AF: 0.0460

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0570 Hom.: 61

Bravo AF: 0.0642

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	8.7
Dann	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10998112; hg19: chr10-70158052;