4-140834736-G-T

Position:

• chr4-140834736-G-T

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 0.805 in 152,156 control chromosomes in the GnomAD database, including 54,479 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 0.80 (54479 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.140834736G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122435 AN: 152038 Hom.: 54469 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.805 AC: 122485 AN: 152156 Hom.: 54479 Cov.: 32 AF XY: 0.809 AC XY: 60204 AN XY: 74390

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.945

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.855

Alfa AF: 0.928 Hom.: 24200

Bravo AF: 0.782

Asia WGS AF: 0.881 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872861; hg19: chr4-141755890;