rs926692

Positions:

• chr20-48454028-A-C
• chr20-48454028-A-G
• chr20-48454028-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 0.575 in 152,038 control chromosomes in the GnomAD database, including 26,143 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 0.57 (26143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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: 0.575 AC: 87282 AN: 151918 Hom.: 26085 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.575 AC: 87398 AN: 152038 Hom.: 26143 Cov.: 32 AF XY: 0.579 AC XY: 43030 AN XY: 74334

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.549

Alfa AF: 0.538 Hom.: 2820

Bravo AF: 0.596

Asia WGS AF: 0.646 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926692; hg19: chr20-47082274;