rs8124695

Positions:

• chr20-40399796-C-A
• chr20-40399796-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 0.124 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;