rs7576183

Variant names:

• chr2-120356687-G-A
• rs7576183

Your query was ambiguous. Multiple possible variants found:

• chr2-120356687-G-A
• chr2-120356687-G-C
• chr2-120356687-G-T

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 0.466 in 146,214 control chromosomes in the GnomAD database, including 15,757 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 0.47 (15757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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: 0.466 AC: 68103 AN: 146108 Hom.: 15742 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.466 AC: 68156 AN: 146214 Hom.: 15757 Cov.: 32 AF XY: 0.475 AC XY: 33961 AN XY: 71556

African (AFR) AF: 0.563 AC: 20374 AN: 36162

American (AMR) AF: 0.426 AC: 6369 AN: 14968

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1282 AN: 3452

East Asian (EAS) AF: 0.718 AC: 3692 AN: 5144

South Asian (SAS) AF: 0.683 AC: 3291 AN: 4816

European-Finnish (FIN) AF: 0.435 AC: 4603 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 143 AN: 288

European-Non Finnish (NFE) AF: 0.399 AC: 27099 AN: 67868

Other (OTH) AF: 0.445 AC: 907 AN: 2040

Alfa AF: 0.416 Hom.: 17179

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.077
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7576183; hg19: chr2-121114263;