rs4730273

Variant names:

• chr7-107839074-C-A
• rs4730273

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 0.261 in 152,092 control chromosomes in the GnomAD database, including 5,462 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 0.26 (5462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.261 AC: 39726 AN: 151972 Hom.: 5454 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.261 AC: 39749 AN: 152092 Hom.: 5462 Cov.: 32 AF XY: 0.263 AC XY: 19555 AN XY: 74334

African (AFR) AF: 0.178 AC: 7378 AN: 41490

American (AMR) AF: 0.264 AC: 4042 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1974 AN: 5172

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3344 AN: 10564

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19975 AN: 67984

Other (OTH) AF: 0.259 AC: 547 AN: 2116

Alfa AF: 0.284 Hom.: 29436

Bravo AF: 0.258

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.6
DANN	Benign	0.78
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4730273; hg19: chr7-107479519;