rs415667

chr20-54935451-G-A

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 0.31 in 151,706 control chromosomes in the GnomAD database, including 7,441 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 0.31 (7441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.310 AC: 47013 AN: 151590 Hom.: 7426 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.310 AC: 47061 AN: 151706 Hom.: 7441 Cov.: 32 AF XY: 0.301 AC XY: 22328 AN XY: 74110

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0852

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.315

Alfa AF: 0.326 Hom.: 1008

Bravo AF: 0.314

Asia WGS AF: 0.131 AC: 456 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.1
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs415667; hg19: chr20-53551990;