rs7529794

Variant names:

• chr1-39937698-G-T
• rs7529794

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 0.195 in 152,104 control chromosomes in the GnomAD database, including 3,316 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 0.20 (3316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29700 AN: 151986 Hom.: 3317 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.195 AC: 29710 AN: 152104 Hom.: 3316 Cov.: 32 AF XY: 0.194 AC XY: 14398 AN XY: 74336

African (AFR) AF: 0.122 AC: 5048 AN: 41518

American (AMR) AF: 0.144 AC: 2195 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3462

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5170

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2588 AN: 10566

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17081 AN: 67972

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.240 Hom.: 2340

Bravo AF: 0.182

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.51
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7529794; hg19: chr1-40403370;