rs3787116

Variant names:

• chr20-63478052-G-A
• rs3787116

Your query was ambiguous. Multiple possible variants found:

• chr20-63478052-G-A
• chr20-63478052-G-C

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 0.207 in 152,092 control chromosomes in the GnomAD database, including 3,327 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 0.21 (3327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.207 AC: 31424 AN: 151974 Hom.: 3321 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.207 AC: 31441 AN: 152092 Hom.: 3327 Cov.: 32 AF XY: 0.201 AC XY: 14950 AN XY: 74346

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.224

Alfa AF: 0.231 Hom.: 6869

Bravo AF: 0.211

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3787116; hg19: chr20-62109405; COSMIC: COSV60105805;