chr1-201112815-C-T

Position:

• chr1-201112815-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.507 in 151,940 control chromosomes in the GnomAD database, including 20,751 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.51 (20751 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 O:1
• Conservation: PhyloP100: -3.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 1-201112815-C-T is Benign according to our data. Variant chr1-201112815-C-T is described in ClinVar as [Benign]. Clinvar id is 17627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.201112815C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76987 AN: 151822 Hom.: 20712 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.507 AC: 77075 AN: 151940 Hom.: 20751 Cov.: 31 AF XY: 0.508 AC XY: 37688 AN XY: 74222

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.527

Alfa AF: 0.429 Hom.: 23079

Bravo AF: 0.527

Asia WGS AF: 0.622 AC: 2159 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Thyrotoxic periodic paralysis, susceptibility to, 1 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Mar 01, 2004

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.60
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2281845; hg19: chr1-201081943;