rs2770378

chr20-3072868-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 0.385 in 152,110 control chromosomes in the GnomAD database, including 11,487 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 0.39 (11487 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.459 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: 0.385 AC: 58532 AN: 151992 Hom.: 11480 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.385 AC: 58574 AN: 152110 Hom.: 11487 Cov.: 33 AF XY: 0.381 AC XY: 28304 AN XY: 74364

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.382

Alfa AF: 0.409 Hom.: 11221

Bravo AF: 0.397

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.7
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2770378; hg19: chr20-3053514; COSMIC: COSV54131796;