rs969127

chr20-48300766-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0599 in 151,620 control chromosomes in the GnomAD database, including 594 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 0.060 (594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 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: 0.0597 AC: 9049 AN: 151502 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.00636

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00930

Gnomad OTH AF: 0.0563

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

GnomAD4 genome AF: 0.0599 AC: 9081 AN: 151620 Hom.: 594 Cov.: 32 AF XY: 0.0614 AC XY: 4549 AN XY: 74078

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0612

Gnomad4 ASJ AF: 0.00636

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.00930

Gnomad4 OTH AF: 0.0571

Alfa AF: 0.0353 Hom.: 34

Bravo AF: 0.0670

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
Cadd	Benign	17
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969127; hg19: chr20-46929509;