rs195714

Variant names:

• chr1-24496631-G-A
• rs195714
• ENST00000651433.1:n.125-35C>T

Variant summary

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

The NR_045407.2(RCAN3AS):​n.147-35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,098 control chromosomes in the GnomAD database, including 5,463 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 0.24 (5463 hom., cov: 32)
• Consequence: RCAN3AS NR_045407.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

Genes affected

RCAN3AS (HGNC:39009): (RCAN3 antisense RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_045407.2. 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
	RCAN3AS	NR_045407.2		n.147-35C>T		intron	N/A
	RCAN3AS	NR_045408.2		n.188-35C>T		intron	N/A
	RCAN3AS	NR_045409.2		n.95-35C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RCAN3AS	ENST00000651433.1		n.125-35C>T		intron	N/A
	RCAN3AS	ENST00000651630.1		n.233-35C>T		intron	N/A
	RCAN3AS	ENST00000652048.1		n.166-35C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37212 AN: 151980 Hom.: 5456 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.245 AC: 37231 AN: 152098 Hom.: 5463 Cov.: 32 AF XY: 0.247 AC XY: 18380 AN XY: 74352

African (AFR) AF: 0.0818 AC: 3397 AN: 41542

American (AMR) AF: 0.223 AC: 3402 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1761 AN: 5158

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4824

European-Finnish (FIN) AF: 0.411 AC: 4334 AN: 10554

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21637 AN: 67962

Other (OTH) AF: 0.237 AC: 500 AN: 2112

Alfa AF: 0.282 Hom.: 823

Bravo AF: 0.223

Asia WGS AF: 0.368 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs195714; hg19: chr1-24823121;