rs7539328

Positions:

• chr1-67266920-G-A
• chr1-67266920-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.280

Alfa AF: 0.269 Hom.: 6313

Bravo AF: 0.313

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7539328; hg19: chr1-67732603;