chr1-67266920-G-A

Variant names:

• chr1-67266920-G-A
• rs7539328

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 0.296 in 152,008 control chromosomes in the GnomAD database, including 7,233 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 0.30 (7233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.296 AC: 44954 AN: 151890 Hom.: 7222 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.296 AC: 45002 AN: 152008 Hom.: 7233 Cov.: 32 AF XY: 0.291 AC XY: 21631 AN XY: 74276

African (AFR) AF: 0.412 AC: 17053 AN: 41438

American (AMR) AF: 0.309 AC: 4721 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1191 AN: 5178

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4806

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10550

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17360 AN: 67968

Other (OTH) AF: 0.280 AC: 591 AN: 2114

Alfa AF: 0.285 Hom.: 8938

Bravo AF: 0.313

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.61
DANN	Benign	0.76
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7539328; hg19: chr1-67732603;