rs4277843

Variant names:

• chr4-110856593-A-G
• rs4277843

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.708

Alfa AF: 0.741 Hom.: 5262

Bravo AF: 0.690

Asia WGS AF: 0.787 AC: 2734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4277843; hg19: chr4-111777749;