rs4321143

Variant names:

• chr15-95613139-A-G
• rs4321143

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 0.283 in 152,116 control chromosomes in the GnomAD database, including 6,275 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 0.28 (6275 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.283 AC: 43009 AN: 151998 Hom.: 6265 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.283 AC: 43049 AN: 152116 Hom.: 6275 Cov.: 33 AF XY: 0.274 AC XY: 20382 AN XY: 74358

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.282

Alfa AF: 0.279 Hom.: 7303

Bravo AF: 0.293

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4321143; hg19: chr15-96156368;