rs4293143

Variant names:

• chr11-83110340-T-G
• rs4293143

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 0.23 in 152,242 control chromosomes in the GnomAD database, including 4,539 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 0.23 (4539 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.230 AC: 34947 AN: 152124 Hom.: 4538 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.230 AC: 34961 AN: 152242 Hom.: 4539 Cov.: 33 AF XY: 0.228 AC XY: 16934 AN XY: 74428

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.220

Alfa AF: 0.276 Hom.: 5597

Bravo AF: 0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4293143; hg19: chr11-82821382;