20-16675319-C-T

Position:

• chr20-16675319-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 0.523 in 152,000 control chromosomes in the GnomAD database, including 20,857 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 0.52 (20857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (NFE) allele frequency at 95% confidence interval = 0.545 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: 0.523 AC: 79495 AN: 151882 Hom.: 20835 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.523 AC: 79558 AN: 152000 Hom.: 20857 Cov.: 32 AF XY: 0.521 AC XY: 38721 AN XY: 74278

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.514

Alfa AF: 0.542 Hom.: 36740

Bravo AF: 0.523

Asia WGS AF: 0.510 AC: 1772 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	0.76
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885567; hg19: chr20-16655964;