rs2529445

Variant names:

• chr7-30490341-A-G
• rs2529445

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 0.237 in 152,160 control chromosomes in the GnomAD database, including 4,781 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 (4781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.237 AC: 35965 AN: 152042 Hom.: 4773 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.237 AC: 36004 AN: 152160 Hom.: 4781 Cov.: 32 AF XY: 0.236 AC XY: 17539 AN XY: 74396

African (AFR) AF: 0.336 AC: 13954 AN: 41498

American (AMR) AF: 0.171 AC: 2609 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1875 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1368 AN: 4828

European-Finnish (FIN) AF: 0.175 AC: 1858 AN: 10592

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12956 AN: 67992

Other (OTH) AF: 0.258 AC: 545 AN: 2110

Alfa AF: 0.214 Hom.: 6600

Bravo AF: 0.243

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.82
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs2529445; hg19: chr7-30529957;