chr4-140572807-T-C

Position:

• chr4-140572807-T-C

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: intergenic_region
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.739

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.140572807T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Benign, no assertion criteria provided

literature only

OMIM

Dec 01, 2003

- -

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;