chr13-24748587-A-G

Variant names:

• chr13-24748587-A-G
• rs7335910
• ENST00000831833.1:n.798A>G

Variant summary

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

The ENST00000831833.1(ENSG00000287887):​n.798A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,162 control chromosomes in the GnomAD database, including 5,126 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 0.24 (5126 hom., cov: 33)
• Consequence: ENSG00000287887 ENST00000831833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 3 publications found

Genes affected

ENSG00000287887 (HGNC:):

RNF17 (HGNC:10060): (ring finger protein 17) This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF17	XM_011535152.3	c.-1586+653A>G		intron_variant	Intron 1 of 40		XP_011533454.1
RNF17	XM_011535155.3	c.-322+653A>G		intron_variant	Intron 1 of 39		XP_011533457.1
RNF17	XM_011535156.3	c.-1586+653A>G		intron_variant	Intron 1 of 40		XP_011533458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287887	ENST00000831833.1	n.798A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287887	ENST00000831834.1	n.850A>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000287887	ENST00000662637.2	n.326+653A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36504 AN: 152044 Hom.: 5131 Cov.: 33

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.240 AC: 36499 AN: 152162 Hom.: 5126 Cov.: 33 AF XY: 0.244 AC XY: 18140 AN XY: 74388

African (AFR) AF: 0.0957 AC: 3978 AN: 41550

American (AMR) AF: 0.336 AC: 5140 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2341 AN: 5178

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4812

European-Finnish (FIN) AF: 0.271 AC: 2870 AN: 10582

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18979 AN: 67974

Other (OTH) AF: 0.250 AC: 527 AN: 2104

Alfa AF: 0.273 Hom.: 3295

Bravo AF: 0.236

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.77
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7335910; hg19: chr13-25322725;