rs2425754

chr20-46159994-G-A

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 0.118 in 152,202 control chromosomes in the GnomAD database, including 1,215 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 0.12 (1215 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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: 0.118 AC: 17930 AN: 152084 Hom.: 1214 Cov.: 33

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.118 AC: 17939 AN: 152202 Hom.: 1215 Cov.: 33 AF XY: 0.118 AC XY: 8761 AN XY: 74414

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0585

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.131

Alfa AF: 0.131 Hom.: 601

Bravo AF: 0.110

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	11
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2425754; hg19: chr20-44788633;