chr2-172727878-C-T

Position:

• chr2-172727878-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026995.1(RAPGEF4-AS1):​n.378-445G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,002 control chromosomes in the GnomAD database, including 3,378 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 0.20 (3378 hom., cov: 33)
• Consequence: RAPGEF4-AS1 NR_026995.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

Genes affected

RAPGEF4-AS1 (HGNC:28081): (RAPGEF4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAPGEF4-AS1	NR_026995.1	n.378-445G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAPGEF4-AS1	ENST00000435328.1	n.378-445G>A		intron_variant, non_coding_transcript_variant		1
RAPGEF4-AS1	ENST00000455435.1	n.65+6427G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29690 AN: 151884 Hom.: 3370 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.196 AC: 29727 AN: 152002 Hom.: 3378 Cov.: 33 AF XY: 0.203 AC XY: 15117 AN XY: 74286

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.183

Alfa AF: 0.184 Hom.: 5502

Bravo AF: 0.186

Asia WGS AF: 0.316 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.010
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349498; hg19: chr2-173592606;