rs8124344

Variant names:

• chr20-240116-C-T
• rs8124344

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 0.174 in 150,750 control chromosomes in the GnomAD database, including 2,657 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 0.17 (2657 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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: 0.174 AC: 26149 AN: 150634 Hom.: 2655 Cov.: 30

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0759

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.174 AC: 26157 AN: 150750 Hom.: 2657 Cov.: 30 AF XY: 0.173 AC XY: 12717 AN XY: 73512

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0759

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.142

Alfa AF: 0.138 Hom.: 292

Bravo AF: 0.176

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8124344; hg19: chr20-220757;