20-20968220-T-C

Position:

• chr20-20968220-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.286 in 152,082 control chromosomes in the GnomAD database, including 7,046 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 0.29 (7046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43521 AN: 151964 Hom.: 7049 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.286 AC: 43530 AN: 152082 Hom.: 7046 Cov.: 32 AF XY: 0.291 AC XY: 21599 AN XY: 74342

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.306

Alfa AF: 0.324 Hom.: 16180

Bravo AF: 0.282

Asia WGS AF: 0.438 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	13
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6137194; hg19: chr20-20948861;