4-42856436-A-G

Variant names:

• chr4-42856436-A-G
• rs9985652

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 0.753 in 152,124 control chromosomes in the GnomAD database, including 44,992 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 0.75 (44992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 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: 0.753 AC: 114479 AN: 152006 Hom.: 44979 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.753 AC: 114538 AN: 152124 Hom.: 44992 Cov.: 32 AF XY: 0.750 AC XY: 55783 AN XY: 74356

African (AFR) AF: 0.536 AC: 22224 AN: 41476

American (AMR) AF: 0.790 AC: 12079 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3154 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2830 AN: 5160

South Asian (SAS) AF: 0.643 AC: 3100 AN: 4820

European-Finnish (FIN) AF: 0.874 AC: 9258 AN: 10594

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59299 AN: 68000

Other (OTH) AF: 0.793 AC: 1674 AN: 2112

Alfa AF: 0.835 Hom.: 228837

Bravo AF: 0.740

Asia WGS AF: 0.618 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9985652; hg19: chr4-42858453;