chr1-213737151-T-G

Position:

• chr1-213737151-T-G

Variant summary

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

The ENST00000456240.1(ENSG00000228255):​n.143+5593T>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 0.812 in 152,242 control chromosomes in the GnomAD database, including 50,942 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 0.81 (50942 hom., cov: 33)
• Consequence: ENST00000456240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS6KC1	XR_007058661.1	n.3886+5593T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000456240.1	n.143+5593T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123602 AN: 152124 Hom.: 50906 Cov.: 33

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.812 AC: 123690 AN: 152242 Hom.: 50942 Cov.: 33 AF XY: 0.811 AC XY: 60347 AN XY: 74430

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.811

Alfa AF: 0.743 Hom.: 16272

Bravo AF: 0.825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1704198; hg19: chr1-213910494;