rs729068

Variant names:

• chr7-128929507-C-T
• rs729068

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 0.24 in 152,130 control chromosomes in the GnomAD database, including 5,206 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 (5206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 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: 0.240 AC: 36489 AN: 152014 Hom.: 5210 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.240 AC: 36476 AN: 152130 Hom.: 5206 Cov.: 32 AF XY: 0.241 AC XY: 17901 AN XY: 74364

African (AFR) AF: 0.119 AC: 4954 AN: 41514

American (AMR) AF: 0.183 AC: 2794 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.0859 AC: 445 AN: 5180

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4832

European-Finnish (FIN) AF: 0.339 AC: 3591 AN: 10598

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

European-Non Finnish (NFE) AF: 0.320 AC: 21707 AN: 67932

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.217 Hom.: 1930

Bravo AF: 0.221

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.73
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs729068; hg19: chr7-128569561;