rs12759209

Positions:

• chr1-213693351-T-C

Variant summary

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

The XR_007058661.1(RPS6KC1):​n.3745-38066T>C 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 0.131 in 152,232 control chromosomes in the GnomAD database, including 1,441 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 0.13 (1441 hom., cov: 33)
• Consequence: RPS6KC1 XR_007058661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

RPS6KC1 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KC1	XR_007058661.1	n.3745-38066T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19929 AN: 152114 Hom.: 1440 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0946

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.131 AC: 19932 AN: 152232 Hom.: 1441 Cov.: 33 AF XY: 0.128 AC XY: 9549 AN XY: 74436

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0291

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.131

Alfa AF: 0.124 Hom.: 2330

Bravo AF: 0.135

Asia WGS AF: 0.104 AC: 362 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	0.17
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12759209; hg19: chr1-213866694;