chr4-112142370-A-G

Variant names:

• chr4-112142370-A-G
• rs1436136

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 0.592 in 150,888 control chromosomes in the GnomAD database, including 28,512 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 0.59 (28512 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89191 AN: 150772 Hom.: 28467 Cov.: 28

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.592 AC: 89296 AN: 150888 Hom.: 28512 Cov.: 28 AF XY: 0.591 AC XY: 43478 AN XY: 73606

African (AFR) AF: 0.824 AC: 33781 AN: 40980

American (AMR) AF: 0.646 AC: 9809 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3468

East Asian (EAS) AF: 0.823 AC: 4218 AN: 5124

South Asian (SAS) AF: 0.464 AC: 2218 AN: 4780

European-Finnish (FIN) AF: 0.436 AC: 4463 AN: 10238

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31003 AN: 67822

Other (OTH) AF: 0.590 AC: 1235 AN: 2092

Alfa AF: 0.500 Hom.: 12046

Bravo AF: 0.625

Asia WGS AF: 0.607 AC: 2107 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs1436136; hg19: chr4-113063526;