ENST00000454736.2:n.200+1820C>T

Variant names:

• chr1-19816373-C-T
• rs3806308
• ENST00000454736.2:n.200+1820C>T

Variant summary

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

The ENST00000454736.2(RNF186-AS1):​n.200+1820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,276 control chromosomes in the GnomAD database, including 10,325 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 0.36 (10325 hom., cov: 34)
• Consequence: RNF186-AS1 ENST00000454736.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 39 publications found

Genes affected

RNF186-AS1 (HGNC:41127): (RNF186 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF186-AS1	NR_186008.1	n.145+1820C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF186-AS1	ENST00000454736.2	n.200+1820C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55018 AN: 152158 Hom.: 10313 Cov.: 34

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.362 AC: 55065 AN: 152276 Hom.: 10325 Cov.: 34 AF XY: 0.364 AC XY: 27126 AN XY: 74456

African (AFR) AF: 0.279 AC: 11580 AN: 41558

American (AMR) AF: 0.433 AC: 6630 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2507 AN: 5184

South Asian (SAS) AF: 0.362 AC: 1749 AN: 4828

European-Finnish (FIN) AF: 0.426 AC: 4516 AN: 10606

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26029 AN: 68012

Other (OTH) AF: 0.350 AC: 740 AN: 2116

Alfa AF: 0.374 Hom.: 35766

Bravo AF: 0.357

Asia WGS AF: 0.493 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.12
DANN	Benign	0.76
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3806308; hg19: chr1-20142866;