rs4812712

Positions:

• chr20-43476299-C-A

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 0.34 in 152,076 control chromosomes in the GnomAD database, including 11,265 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 0.34 (11265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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: 0.340 AC: 51657 AN: 151958 Hom.: 11228 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.340 AC: 51762 AN: 152076 Hom.: 11265 Cov.: 32 AF XY: 0.339 AC XY: 25214 AN XY: 74342

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.285

Alfa AF: 0.241 Hom.: 7016

Bravo AF: 0.357

Asia WGS AF: 0.280 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4812712; hg19: chr20-42104939;