chr1-100253574-C-T

Position:

• chr1-100253574-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

RTCA-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.100253574C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RTCA-AS1	ENST00000650038.1	n.622G>A		non_coding_transcript_exon_variant	4/4

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.389

Alfa AF: 0.358 Hom.: 972

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12060945; hg19: chr1-100719130;