4-140569265-T-G

Position:

• chr4-140569265-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.376 in 152,162 control chromosomes in the GnomAD database, including 12,669 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (12669 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.140569265T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57066 AN: 152044 Hom.: 12645 Cov.: 33

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.376 AC: 57140 AN: 152162 Hom.: 12669 Cov.: 33 AF XY: 0.378 AC XY: 28132 AN XY: 74372

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.354

Alfa AF: 0.294 Hom.: 4324

Bravo AF: 0.394

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
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: rs3811787; hg19: chr4-141490419;