rs10498058

Variant names:

• chr2-218042359-C-T
• rs10498058
• ENST00000457754.6:n.-1158+6965C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457754.6(RUFY4):​n.-1158+6965C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 152,230 control chromosomes in the GnomAD database, including 2,363 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 0.10 (2363 hom., cov: 33)
• Consequence: RUFY4 ENST00000457754.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 0 publications found

Genes affected

RUFY4 (HGNC:24804): (RUN and FYVE domain containing 4) Enables phosphatidylinositol-3-phosphate binding activity. Involved in autophagosome assembly; cellular response to interleukin-4; and positive regulation of macroautophagy. Located in autophagosome. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUFY4	NR_034176.2	n.329+6965C>T		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUFY4	ENST00000457754.6	n.-1158+6965C>T		intron_variant	Intron 2 of 13	2		ENSP00000410091.2
RUFY4	ENST00000463618.6	n.194+6965C>T		intron_variant	Intron 2 of 5	5
RUFY4	ENST00000465568.5	n.89+7175C>T		intron_variant	Intron 1 of 5	5
RUFY4	ENST00000497857.5	n.435+6965C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15118 AN: 152112 Hom.: 2351 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00176

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0996 AC: 15164 AN: 152230 Hom.: 2363 Cov.: 33 AF XY: 0.0966 AC XY: 7192 AN XY: 74446

African (AFR) AF: 0.336 AC: 13918 AN: 41478

American (AMR) AF: 0.0421 AC: 644 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3472

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5190

South Asian (SAS) AF: 0.0462 AC: 223 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00178 AC: 121 AN: 68020

Other (OTH) AF: 0.0780 AC: 165 AN: 2116

Alfa AF: 0.0593 Hom.: 177

Bravo AF: 0.112

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.33
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10498058; hg19: chr2-218907082;