1-201112815-C-T

Variant names:

• chr1-201112815-C-T
• rs2281845

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 O:1
• Conservation: PhyloP100: -3.24
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.679 AC: 28143 AN: 41432

American (AMR) AF: 0.525 AC: 8023 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1278 AN: 3466

East Asian (EAS) AF: 0.744 AC: 3828 AN: 5148

South Asian (SAS) AF: 0.493 AC: 2372 AN: 4810

European-Finnish (FIN) AF: 0.385 AC: 4059 AN: 10552

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27723 AN: 67924

Other (OTH) AF: 0.527 AC: 1114 AN: 2112

Alfa AF: 0.443 Hom.: 54024

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

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Thyrotoxic periodic paralysis, susceptibility to, 1 Other:1

Mar 01, 2004

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.60
DANN	Benign	0.77
PhyloP100		-3.2
PromoterAI		0.0085	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2281845; hg19: chr1-201081943;