chr4-43685157-T-G

Variant names:

• chr4-43685157-T-G
• rs1594934

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 0.876 in 151,798 control chromosomes in the GnomAD database, including 58,449 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 0.88 (58449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 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: 0.876 AC: 132850 AN: 151680 Hom.: 58384 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.876 AC: 132972 AN: 151798 Hom.: 58449 Cov.: 31 AF XY: 0.873 AC XY: 64744 AN XY: 74192

African (AFR) AF: 0.916 AC: 38003 AN: 41478

American (AMR) AF: 0.760 AC: 11548 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2931 AN: 3466

East Asian (EAS) AF: 0.747 AC: 3823 AN: 5116

South Asian (SAS) AF: 0.790 AC: 3806 AN: 4818

European-Finnish (FIN) AF: 0.948 AC: 10065 AN: 10620

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 59898 AN: 67790

Other (OTH) AF: 0.850 AC: 1791 AN: 2106

Alfa AF: 0.889 Hom.: 7777

Bravo AF: 0.861

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.50
DANN	Benign	0.77
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1594934; hg19: chr4-43687174;