20-43406210-A-C

Position:

• chr20-43406210-A-C

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 0.28 in 152,088 control chromosomes in the GnomAD database, including 6,024 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 (6024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42523 AN: 151970 Hom.: 5995 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.280 AC: 42594 AN: 152088 Hom.: 6024 Cov.: 32 AF XY: 0.274 AC XY: 20406 AN XY: 74340

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.286

Alfa AF: 0.288 Hom.: 1129

Bravo AF: 0.278

Asia WGS AF: 0.158 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6030844; hg19: chr20-42034850;