2-120360548-T-C

Variant names:

• chr2-120360548-T-C
• rs7579169

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 0.68 in 152,106 control chromosomes in the GnomAD database, including 35,772 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 0.68 (35772 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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: 0.680 AC: 103358 AN: 151988 Hom.: 35740 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.680 AC: 103444 AN: 152106 Hom.: 35772 Cov.: 33 AF XY: 0.682 AC XY: 50698 AN XY: 74344

African (AFR) AF: 0.818 AC: 33934 AN: 41508

American (AMR) AF: 0.654 AC: 10010 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2333 AN: 3470

East Asian (EAS) AF: 0.762 AC: 3928 AN: 5152

South Asian (SAS) AF: 0.602 AC: 2902 AN: 4818

European-Finnish (FIN) AF: 0.655 AC: 6932 AN: 10576

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41205 AN: 67972

Other (OTH) AF: 0.684 AC: 1444 AN: 2112

Alfa AF: 0.635 Hom.: 37988

Bravo AF: 0.688

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.55
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7579169; hg19: chr2-121118124;