rs531043

Variant names:

• chr20-4406793-C-A
• rs531043

Your query was ambiguous. Multiple possible variants found:

• chr20-4406793-C-A
• chr20-4406793-C-G
• chr20-4406793-C-T

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 0.821 in 152,120 control chromosomes in the GnomAD database, including 51,368 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 0.82 (51368 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 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: 0.821 AC: 124803 AN: 152002 Hom.: 51323 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.821 AC: 124907 AN: 152120 Hom.: 51368 Cov.: 31 AF XY: 0.821 AC XY: 61081 AN XY: 74358

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.820

Alfa AF: 0.830 Hom.: 21657

Bravo AF: 0.818

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531043; hg19: chr20-4387440;