rs17115674

Variant names:

• chr14-44870240-T-A
• rs17115674
• ENST00000715832.1:n.52+26772A>T

Your query was ambiguous. Multiple possible variants found:

• chr14-44870240-T-A
• chr14-44870240-T-C

Variant summary

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

The ENST00000715832.1(RRAGAP1-AS1):​n.52+26772A>T variant causes a intron 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: 31)
• Consequence: RRAGAP1-AS1 ENST00000715832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 1 publications found

Genes affected

RRAGAP1-AS1 (HGNC:55445): (RRAGAP1 antisense RNA 1)

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=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RRAGAP1-AS1	ENST00000715832.1	n.52+26772A>T		intron_variant	Intron 1 of 7
RRAGAP1-AS1	ENST00000715833.1	n.365+28990A>T		intron_variant	Intron 3 of 7
RRAGAP1-AS1	ENST00000780005.1	n.365+28990A>T		intron_variant	Intron 3 of 6
RRAGAP1-AS1	ENST00000780006.1	n.236+28990A>T		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs17115674; hg19: chr14-45339443;