3-143185270-C-G

Variant names:

• chr3-143185270-C-G
• rs54520

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 0.748 in 152,190 control chromosomes in the GnomAD database, including 42,993 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 0.75 (42993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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: 0.748 AC: 113739 AN: 152072 Hom.: 42958 Cov.: 33

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.748 AC: 113824 AN: 152190 Hom.: 42993 Cov.: 33 AF XY: 0.745 AC XY: 55423 AN XY: 74406

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.728

Alfa AF: 0.654 Hom.: 1888

Bravo AF: 0.761

Asia WGS AF: 0.658 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs54520; hg19: chr3-142904112;