chr2-121820466-A-G

Variant names:

• chr2-121820466-A-G
• rs7577075

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 0.745 in 152,172 control chromosomes in the GnomAD database, including 43,499 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 0.75 (43499 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113288 AN: 152054 Hom.: 43456 Cov.: 34

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.745 AC: 113386 AN: 152172 Hom.: 43499 Cov.: 34 AF XY: 0.733 AC XY: 54529 AN XY: 74380

African (AFR) AF: 0.780 AC: 32402 AN: 41516

American (AMR) AF: 0.632 AC: 9663 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2911 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1015 AN: 5172

South Asian (SAS) AF: 0.726 AC: 3504 AN: 4828

European-Finnish (FIN) AF: 0.655 AC: 6936 AN: 10582

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54373 AN: 67994

Other (OTH) AF: 0.766 AC: 1619 AN: 2114

Alfa AF: 0.791 Hom.: 28009

Bravo AF: 0.739

Asia WGS AF: 0.515 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.29
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7577075; hg19: chr2-122578042;