rs729302

Variant names:

• chr7-128928906-A-C
• rs729302

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 0.28 in 152,068 control chromosomes in the GnomAD database, including 6,444 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 0.28 (6444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 79 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 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: 0.280 AC: 42603 AN: 151950 Hom.: 6443 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.280 AC: 42619 AN: 152068 Hom.: 6444 Cov.: 32 AF XY: 0.283 AC XY: 21004 AN XY: 74322

African (AFR) AF: 0.199 AC: 8258 AN: 41496

American (AMR) AF: 0.218 AC: 3326 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1623 AN: 5152

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4816

European-Finnish (FIN) AF: 0.351 AC: 3719 AN: 10594

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22247 AN: 67938

Other (OTH) AF: 0.255 AC: 538 AN: 2110

Alfa AF: 0.310 Hom.: 33437

Bravo AF: 0.267

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.1
DANN	Benign	0.74
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs729302; hg19: chr7-128568960;