2-61541286-A-C

Variant names:

• chr2-61541286-A-C
• rs1562308

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 0.631 in 151,476 control chromosomes in the GnomAD database, including 30,353 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 0.63 (30353 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.631 AC: 95493 AN: 151358 Hom.: 30313 Cov.: 29

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.631 AC: 95588 AN: 151476 Hom.: 30353 Cov.: 29 AF XY: 0.631 AC XY: 46670 AN XY: 73986

African (AFR) AF: 0.686 AC: 28324 AN: 41300

American (AMR) AF: 0.586 AC: 8898 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3337 AN: 5140

South Asian (SAS) AF: 0.612 AC: 2950 AN: 4818

European-Finnish (FIN) AF: 0.601 AC: 6235 AN: 10376

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41301 AN: 67886

Other (OTH) AF: 0.653 AC: 1372 AN: 2100

Alfa AF: 0.515 Hom.: 1857

Bravo AF: 0.633

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.51
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1562308; hg19: chr2-61768421;