rs10494962

Positions:

• chr1-213727915-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007058661.1(RPS6KC1):​n.3745-3502A>G 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 0.283 in 152,056 control chromosomes in the GnomAD database, including 6,913 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 0.28 (6913 hom., cov: 32)
• Consequence: RPS6KC1 XR_007058661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

RPS6KC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KC1	XR_007058661.1	n.3745-3502A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42978 AN: 151938 Hom.: 6905 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.283 AC: 43006 AN: 152056 Hom.: 6913 Cov.: 32 AF XY: 0.278 AC XY: 20639 AN XY: 74352

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.0578

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.272

Alfa AF: 0.257 Hom.: 940

Bravo AF: 0.293

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494962; hg19: chr1-213901258;