chr20-47947062-A-T

Position:

• chr20-47947062-A-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 0.0979 in 152,212 control chromosomes in the GnomAD database, including 1,102 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 0.098 (1102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.0977 AC: 14865 AN: 152094 Hom.: 1099 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0446

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.0979 AC: 14894 AN: 152212 Hom.: 1102 Cov.: 32 AF XY: 0.0994 AC XY: 7395 AN XY: 74428

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.0446

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.0916

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0712

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.0827 Hom.: 80

Bravo AF: 0.103

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10211734; hg19: chr20-46575806;