rs10494961

chr1-213573561-C-G

Variant summary

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

The ENST00000417161.2(ENSG00000225233):n.454-5218C>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 0.235 in 152,134 control chromosomes in the GnomAD database, including 4,370 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 0.23 (4370 hom., cov: 33)
• Consequence: ENST00000417161.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KC1	XR_007058661.1	n.3744+27114C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000417161.2	n.454-5218C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35702 AN: 152016 Hom.: 4364 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.235 AC: 35734 AN: 152134 Hom.: 4370 Cov.: 33 AF XY: 0.235 AC XY: 17466 AN XY: 74366

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.220

Alfa AF: 0.219 Hom.: 468

Bravo AF: 0.239

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	13
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494961; hg19: chr1-213746904;