chr20-48150492-C-T

Position:

• chr20-48150492-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 0.427 in 152,118 control chromosomes in the GnomAD database, including 14,452 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 0.43 (14452 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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 = 0.494 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: 0.427 AC: 64936 AN: 152000 Hom.: 14436 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.427 AC: 64983 AN: 152118 Hom.: 14452 Cov.: 33 AF XY: 0.424 AC XY: 31566 AN XY: 74370

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.404

Alfa AF: 0.471 Hom.: 19861

Bravo AF: 0.414

Asia WGS AF: 0.319 AC: 1111 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	0.0020
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11086243; hg19: chr20-46779235;