chr4-140834736-G-T

Variant names:

• chr4-140834736-G-T
• rs1872861

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.387 AC: 16049 AN: 41432

American (AMR) AF: 0.908 AC: 13884 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3281 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4973 AN: 5176

South Asian (SAS) AF: 0.919 AC: 4436 AN: 4826

European-Finnish (FIN) AF: 0.964 AC: 10231 AN: 10618

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66642 AN: 68028

Other (OTH) AF: 0.855 AC: 1807 AN: 2114

Alfa AF: 0.932 Hom.: 47483

Bravo AF: 0.782

Asia WGS AF: 0.881 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1872861; hg19: chr4-141755890;