chr2-61545122-A-G

Variant names:

• chr2-61545122-A-G
• rs6545883

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 0.586 in 152,080 control chromosomes in the GnomAD database, including 26,315 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 0.59 (26315 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89129 AN: 151960 Hom.: 26301 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.586 AC: 89192 AN: 152080 Hom.: 26315 Cov.: 33 AF XY: 0.589 AC XY: 43771 AN XY: 74342

African (AFR) AF: 0.532 AC: 22063 AN: 41460

American (AMR) AF: 0.564 AC: 8618 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2331 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3360 AN: 5186

South Asian (SAS) AF: 0.614 AC: 2965 AN: 4828

European-Finnish (FIN) AF: 0.602 AC: 6363 AN: 10572

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41357 AN: 67978

Other (OTH) AF: 0.620 AC: 1309 AN: 2110

Alfa AF: 0.604 Hom.: 67216

Bravo AF: 0.583

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.9
DANN	Benign	0.66
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs6545883; hg19: chr2-61772257;