chr10-68398295-T-C

Variant names:

• chr10-68398295-T-C
• rs10998112
• NM_001330103.2:c.297-1414A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RUFY2	NM_001330103.2	c.297-1414A>G		intron_variant	Intron 3 of 17	ENST00000602465.6	NP_001317032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUFY2	ENST00000602465.6	c.297-1414A>G		intron_variant	Intron 3 of 17	5	NM_001330103.2	ENSP00000473462.1

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

African (AFR) AF: 0.110 AC: 4556 AN: 41528

American (AMR) AF: 0.0348 AC: 531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00890 AC: 43 AN: 4830

European-Finnish (FIN) AF: 0.0460 AC: 487 AN: 10590

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0481 AC: 3273 AN: 68022

Other (OTH) AF: 0.0498 AC: 105 AN: 2108

Alfa AF: 0.0589 Hom.: 65

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
PhyloP100		0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10998112; hg19: chr10-70158052;