chr20-40399796-C-A

Variant names:

• chr20-40399796-C-A
• rs8124695

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 0.124 in 152,046 control chromosomes in the GnomAD database, including 1,743 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 0.12 (1743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 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: 0.124 AC: 18826 AN: 151928 Hom.: 1736 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.124 AC: 18864 AN: 152046 Hom.: 1743 Cov.: 31 AF XY: 0.120 AC XY: 8907 AN XY: 74330

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0805 Hom.: 1019

Bravo AF: 0.133

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
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: rs8124695; hg19: chr20-39028436;