rs969127

Variant names:

• chr20-48300766-C-T
• rs969127

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;