2-120360455-A-G

Variant names:

• chr2-120360455-A-G
• rs7576192

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 0.681 in 152,024 control chromosomes in the GnomAD database, including 35,784 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 (35784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.681 AC: 103381 AN: 151906 Hom.: 35753 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.681 AC: 103466 AN: 152024 Hom.: 35784 Cov.: 32 AF XY: 0.682 AC XY: 50701 AN XY: 74290

African (AFR) AF: 0.816 AC: 33877 AN: 41504

American (AMR) AF: 0.654 AC: 9996 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2334 AN: 3470

East Asian (EAS) AF: 0.763 AC: 3934 AN: 5158

South Asian (SAS) AF: 0.602 AC: 2904 AN: 4820

European-Finnish (FIN) AF: 0.658 AC: 6943 AN: 10558

Middle Eastern (MID) AF: 0.683 AC: 198 AN: 290

European-Non Finnish (NFE) AF: 0.608 AC: 41276 AN: 67926

Other (OTH) AF: 0.684 AC: 1441 AN: 2106

Alfa AF: 0.651 Hom.: 4724

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	-0.95
CADD	Benign	0.75
DANN	Benign	0.51
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs7576192; hg19: chr2-121118031;