rs2108130

Variant names:

• chr7-28922563-C-A
• rs2108130

Your query was ambiguous. Multiple possible variants found:

• chr7-28922563-C-A
• chr7-28922563-C-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 0.244 in 152,054 control chromosomes in the GnomAD database, including 4,938 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 0.24 (4938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.244 AC: 37124 AN: 151934 Hom.: 4929 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.244 AC: 37166 AN: 152054 Hom.: 4938 Cov.: 32 AF XY: 0.243 AC XY: 18051 AN XY: 74338

African (AFR) AF: 0.337 AC: 13952 AN: 41442

American (AMR) AF: 0.233 AC: 3560 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.0788 AC: 408 AN: 5176

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2521 AN: 10564

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14336 AN: 67994

Other (OTH) AF: 0.229 AC: 482 AN: 2106

Alfa AF: 0.179 Hom.: 547

Bravo AF: 0.248

Asia WGS AF: 0.176 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs2108130; hg19: chr7-28962180;