chr20-16651764-T-C

Position:

• chr20-16651764-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 0.139 in 152,210 control chromosomes in the GnomAD database, including 1,652 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 0.14 (1652 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 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: 0.139 AC: 21203 AN: 152092 Hom.: 1649 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.139 AC: 21219 AN: 152210 Hom.: 1652 Cov.: 33 AF XY: 0.143 AC XY: 10657 AN XY: 74394

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.143

Alfa AF: 0.117 Hom.: 759

Bravo AF: 0.144

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.021
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6135823; hg19: chr20-16632409;