rs2770381

Variant names:

• chr20-3081340-A-C
• rs2770381

Your query was ambiguous. Multiple possible variants found:

• chr20-3081340-A-C
• chr20-3081340-A-T

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 0.355 in 151,982 control chromosomes in the GnomAD database, including 10,161 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 0.36 (10161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 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: 0.356 AC: 53994 AN: 151864 Hom.: 10152 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.355 AC: 54026 AN: 151982 Hom.: 10161 Cov.: 31 AF XY: 0.355 AC XY: 26364 AN XY: 74272

African (AFR) AF: 0.240 AC: 9968 AN: 41460

American (AMR) AF: 0.453 AC: 6919 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1728 AN: 5138

South Asian (SAS) AF: 0.309 AC: 1489 AN: 4822

European-Finnish (FIN) AF: 0.370 AC: 3905 AN: 10560

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27696 AN: 67956

Other (OTH) AF: 0.340 AC: 714 AN: 2100

Alfa AF: 0.388 Hom.: 17411

Bravo AF: 0.360

Asia WGS AF: 0.360 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs2770381; hg19: chr20-3061986;