rs4277843

Variant names:

• chr4-110856593-A-G
• rs4277843

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 0.704 in 152,100 control chromosomes in the GnomAD database, including 38,995 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 0.70 (38995 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107056 AN: 151982 Hom.: 38988 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.704 AC: 107087 AN: 152100 Hom.: 38995 Cov.: 33 AF XY: 0.713 AC XY: 52991 AN XY: 74356

African (AFR) AF: 0.499 AC: 20692 AN: 41468

American (AMR) AF: 0.764 AC: 11678 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2761 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4326 AN: 5172

South Asian (SAS) AF: 0.831 AC: 4010 AN: 4826

European-Finnish (FIN) AF: 0.827 AC: 8750 AN: 10580

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52442 AN: 67986

Other (OTH) AF: 0.708 AC: 1498 AN: 2116

Alfa AF: 0.732 Hom.: 5371

Bravo AF: 0.690

Asia WGS AF: 0.787 AC: 2734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4277843; hg19: chr4-111777749;