4-140834736-G-T

Variant names:

• chr4-140834736-G-T
• rs1872861

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;