1-100253574-C-T

Variant names:

• chr1-100253574-C-T
• rs12060945
• ENST00000650038.1:n.622G>A

Variant summary

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

The ENST00000650038.1(RTCA-AS1):​n.622G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,088 control chromosomes in the GnomAD database, including 11,387 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 0.37 (11387 hom., cov: 34)
• Consequence: RTCA-AS1 ENST00000650038.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 3 publications found

Genes affected

RTCA-AS1 (HGNC:50573): (RTCA antisense RNA 1)

ENSG00000285530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTCA-AS1	ENST00000650038.1	n.622G>A		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000285530	ENST00000648283.1	n.*160C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56118 AN: 151970 Hom.: 11393 Cov.: 34

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.369 AC: 56102 AN: 152088 Hom.: 11387 Cov.: 34 AF XY: 0.372 AC XY: 27651 AN XY: 74346

African (AFR) AF: 0.209 AC: 8664 AN: 41482

American (AMR) AF: 0.421 AC: 6436 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3378 AN: 5172

South Asian (SAS) AF: 0.384 AC: 1853 AN: 4822

European-Finnish (FIN) AF: 0.451 AC: 4772 AN: 10570

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 27994 AN: 67974

Other (OTH) AF: 0.389 AC: 822 AN: 2114

Alfa AF: 0.399 Hom.: 35630

Bravo AF: 0.365

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs12060945; hg19: chr1-100719130;