14-44870240-T-C

Variant names:

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

Variant summary

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

The ENST00000715832.1(RRAGAP1-AS1):​n.52+26772A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,232 control chromosomes in the GnomAD database, including 615 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 0.078 (615 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715832.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RRAGAP1-AS1	ENST00000715832.1		n.52+26772A>G		intron	N/A
	RRAGAP1-AS1	ENST00000715833.1		n.365+28990A>G		intron	N/A
	RRAGAP1-AS1	ENST00000780005.1		n.365+28990A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11838 AN: 152114 Hom.: 615 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0549

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0778 AC: 11849 AN: 152232 Hom.: 615 Cov.: 31 AF XY: 0.0799 AC XY: 5947 AN XY: 74430

African (AFR) AF: 0.140 AC: 5815 AN: 41512

American (AMR) AF: 0.0546 AC: 836 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.114 AC: 592 AN: 5176

South Asian (SAS) AF: 0.108 AC: 522 AN: 4826

European-Finnish (FIN) AF: 0.0779 AC: 826 AN: 10604

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0399 AC: 2713 AN: 68020

Other (OTH) AF: 0.0718 AC: 152 AN: 2116

Alfa AF: 0.0575 Hom.: 102

Bravo AF: 0.0794

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.62
PhyloP100		-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17115674;

hg19: chr14-45339443;