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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	-	Thyrotoxic periodic paralysis, susceptibility to, 1 (1)

Computational scores

Source: dbNSFP v4.9

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;