rs2060390

Variant names:

• chr2-26801610-G-A
• rs2060390

Your query was ambiguous. Multiple possible variants found:

• chr2-26801610-G-A
• chr2-26801610-G-C

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 0.737 in 152,164 control chromosomes in the GnomAD database, including 41,676 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 0.74 (41676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 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: 0.737 AC: 112107 AN: 152046 Hom.: 41642 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.737 AC: 112195 AN: 152164 Hom.: 41676 Cov.: 32 AF XY: 0.729 AC XY: 54226 AN XY: 74372

African (AFR) AF: 0.750 AC: 31159 AN: 41530

American (AMR) AF: 0.769 AC: 11740 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2437 AN: 5164

South Asian (SAS) AF: 0.564 AC: 2720 AN: 4824

European-Finnish (FIN) AF: 0.705 AC: 7459 AN: 10586

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.757 AC: 51509 AN: 68004

Other (OTH) AF: 0.751 AC: 1587 AN: 2112

Alfa AF: 0.749 Hom.: 136505

Bravo AF: 0.745

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.43
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2060390; hg19: chr2-27024478;