14-44845780-G-A

Variant names:

• chr14-44845780-G-A
• rs7143583
• ENST00000715832.1:n.53-14090C>T

Variant summary

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

The ENST00000715832.1(RRAGAP1-AS1):​n.53-14090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,098 control chromosomes in the GnomAD database, including 1,860 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 0.15 (1860 hom., cov: 32)
• Consequence: RRAGAP1-AS1 ENST00000715832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 6 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=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RRAGAP1-AS1	ENST00000715832.1		n.53-14090C>T		intron	N/A
	RRAGAP1-AS1	ENST00000715833.1		n.366-14090C>T		intron	N/A
	RRAGAP1-AS1	ENST00000780005.1		n.366-14090C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22288 AN: 151980 Hom.: 1859 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.147 AC: 22313 AN: 152098 Hom.: 1860 Cov.: 32 AF XY: 0.146 AC XY: 10895 AN XY: 74370

African (AFR) AF: 0.0747 AC: 3100 AN: 41492

American (AMR) AF: 0.184 AC: 2815 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3470

East Asian (EAS) AF: 0.106 AC: 547 AN: 5174

South Asian (SAS) AF: 0.206 AC: 990 AN: 4808

European-Finnish (FIN) AF: 0.137 AC: 1451 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12198 AN: 67984

Other (OTH) AF: 0.185 AC: 389 AN: 2108

Alfa AF: 0.174 Hom.: 8301

Bravo AF: 0.149

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	7.0
DANN	Benign	0.52
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7143583; hg19: chr14-45314983;