rs17706439

Positions:

• chr1-213682245-G-A

Variant summary

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

The XR_007058661.1(RPS6KC1):​n.3745-49172G>A 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 0.134 in 152,122 control chromosomes in the GnomAD database, including 1,495 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 (1495 hom., cov: 32)
• Consequence: RPS6KC1 XR_007058661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

RPS6KC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS6KC1	XR_007058661.1	n.3745-49172G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20414 AN: 152004 Hom.: 1493 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.134 AC: 20422 AN: 152122 Hom.: 1495 Cov.: 32 AF XY: 0.133 AC XY: 9921 AN XY: 74368

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.120

Alfa AF: 0.138 Hom.: 811

Bravo AF: 0.124

Asia WGS AF: 0.0770 AC: 271 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	2.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17706439; hg19: chr1-213855588;