chr20-40027058-C-T

Position:

• chr20-40027058-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 0.499 in 152,070 control chromosomes in the GnomAD database, including 21,607 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 0.50 (21607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.499 AC: 75899 AN: 151952 Hom.: 21606 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.499 AC: 75895 AN: 152070 Hom.: 21607 Cov.: 32 AF XY: 0.499 AC XY: 37090 AN XY: 74296

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.488

Alfa AF: 0.593 Hom.: 36624

Bravo AF: 0.480

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2224536; hg19: chr20-38655700;