20-5714407-T-C

Position:

• chr20-5714407-T-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 0.188 in 152,174 control chromosomes in the GnomAD database, including 2,840 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 0.19 (2840 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.188 AC: 28536 AN: 152056 Hom.: 2835 Cov.: 30

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.188 AC: 28580 AN: 152174 Hom.: 2840 Cov.: 30 AF XY: 0.187 AC XY: 13911 AN XY: 74376

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.198

Alfa AF: 0.175 Hom.: 2908

Bravo AF: 0.197

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085252; hg19: chr20-5695053;