rs3920632

Positions:

• chr20-6355950-G-A
• chr20-6355950-G-C
• chr20-6355950-G-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 0.298 in 152,128 control chromosomes in the GnomAD database, including 8,132 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 0.30 (8132 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45376 AN: 152008 Hom.: 8126 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.298 AC: 45393 AN: 152128 Hom.: 8132 Cov.: 33 AF XY: 0.309 AC XY: 22954 AN XY: 74354

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.329

Alfa AF: 0.309 Hom.: 8719

Bravo AF: 0.301

Asia WGS AF: 0.522 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
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: rs3920632; hg19: chr20-6336597;