rs1891059

Positions:

• chr1-213772666-G-A
• chr1-213772666-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000456240.1(ENSG00000228255):​n.144-21718G>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 0.0413 in 148,344 control chromosomes in the GnomAD database, including 169 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 0.041 (169 hom., cov: 30)
• Consequence: ENST00000456240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0413 (6134/148344) while in subpopulation NFE AF= 0.0496 (3347/67442). AF 95% confidence interval is 0.0482. There are 169 homozygotes in gnomad4. There are 2878 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 169 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KC1	XR_007058661.1	n.3886+41108G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000456240.1	n.144-21718G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6132 AN: 148234 Hom.: 169 Cov.: 30

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0850

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0688

Gnomad EAS AF: 0.000619

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0915

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0413 AC: 6134 AN: 148344 Hom.: 169 Cov.: 30 AF XY: 0.0399 AC XY: 2878 AN XY: 72158

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.0380

Gnomad4 ASJ AF: 0.0688

Gnomad4 EAS AF: 0.000620

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0614

Gnomad4 NFE AF: 0.0496

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0237 Hom.: 8

Bravo AF: 0.0401

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891059; hg19: chr1-213946009;