rs7335910

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-24748587-A-C
• chr13-24748587-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000831833.1(ENSG00000287887):​n.798A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF17	XM_011535152.3	c.-1586+653A>C		intron_variant	Intron 1 of 40		XP_011533454.1
RNF17	XM_011535155.3	c.-322+653A>C		intron_variant	Intron 1 of 39		XP_011533457.1
RNF17	XM_011535156.3	c.-1586+653A>C		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>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287887	ENST00000831834.1	n.850A>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000287887	ENST00000662637.2	n.326+653A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
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;