4-133645303-A-G

Variant names:

• chr4-133645303-A-G
• rs2713280

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 0.535 in 151,864 control chromosomes in the GnomAD database, including 22,440 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 0.54 (22440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81208 AN: 151746 Hom.: 22417 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.535 AC: 81276 AN: 151864 Hom.: 22440 Cov.: 32 AF XY: 0.528 AC XY: 39172 AN XY: 74238

African (AFR) AF: 0.625 AC: 25871 AN: 41370

American (AMR) AF: 0.482 AC: 7351 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2224 AN: 3466

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5144

South Asian (SAS) AF: 0.563 AC: 2711 AN: 4814

European-Finnish (FIN) AF: 0.379 AC: 4001 AN: 10562

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35979 AN: 67932

Other (OTH) AF: 0.568 AC: 1201 AN: 2114

Alfa AF: 0.521 Hom.: 14820

Bravo AF: 0.544

Asia WGS AF: 0.420 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.87
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2713280; hg19: chr4-134566458;