20-48450711-A-G

Variant names:

• chr20-48450711-A-G
• rs926693

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 0.577 in 151,962 control chromosomes in the GnomAD database, including 26,467 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 0.58 (26467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87617 AN: 151844 Hom.: 26408 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.577 AC: 87732 AN: 151962 Hom.: 26467 Cov.: 32 AF XY: 0.582 AC XY: 43178 AN XY: 74244

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.550

Alfa AF: 0.485 Hom.: 7810

Bravo AF: 0.599

Asia WGS AF: 0.644 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.070
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926693; hg19: chr20-47078957;