chr4-140572807-T-C

Variant names:

• chr4-140572807-T-C
• rs1800592

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.394 in 152,132 control chromosomes in the GnomAD database, including 14,240 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.39 (14240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.739
• Publications: 61 publications found

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 4-140572807-T-C is Benign according to our data. Variant chr4-140572807-T-C is described in ClinVar as Benign. ClinVar VariationId is 17659.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.394 AC: 59821 AN: 152014 Hom.: 14199 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.394 AC: 59918 AN: 152132 Hom.: 14240 Cov.: 32 AF XY: 0.393 AC XY: 29198 AN XY: 74372

African (AFR) AF: 0.664 AC: 27549 AN: 41502

American (AMR) AF: 0.405 AC: 6179 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2522 AN: 5182

South Asian (SAS) AF: 0.372 AC: 1796 AN: 4826

European-Finnish (FIN) AF: 0.217 AC: 2289 AN: 10566

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17262 AN: 67996

Other (OTH) AF: 0.354 AC: 749 AN: 2114

Alfa AF: 0.383 Hom.: 6092

Bravo AF: 0.420

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	UCP1 POLYMORPHISM (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1800592; hg19: chr4-141493961;