chr20-3072868-G-A

Variant names:

• chr20-3072868-G-A
• rs2770378

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.338 AC: 14018 AN: 41514

American (AMR) AF: 0.468 AC: 7159 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1764 AN: 5146

South Asian (SAS) AF: 0.396 AC: 1911 AN: 4828

European-Finnish (FIN) AF: 0.311 AC: 3293 AN: 10598

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27897 AN: 67952

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.406 Hom.: 18937

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
PhyloP100		0.23

Splicing

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

Other links and lift over

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