4-140572807-T-C

Variant names:

• chr4-140572807-T-C
• rs1800592

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 id 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.

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: 0.394 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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.354

Alfa AF: 0.320 Hom.: 1934

Bravo AF: 0.420

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

UCP1 POLYMORPHISM Benign:1

Dec 01, 2003

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800592; hg19: chr4-141493961;