rs879471

chr20-63638589-C-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 0.43 in 152,122 control chromosomes in the GnomAD database, including 15,878 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 0.43 (15878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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: 0.430 AC: 65416 AN: 152002 Hom.: 15880 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.430 AC: 65418 AN: 152122 Hom.: 15878 Cov.: 33 AF XY: 0.424 AC XY: 31512 AN XY: 74358

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.458

Alfa AF: 0.538 Hom.: 31338

Bravo AF: 0.421

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.35
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879471; hg19: chr20-62269942;