rs5745946

chr1-12166728-AGGGCAGGTGGAGGCC-Achr1-12166728-AGGGCAGGTGGAGGCC-AGGGCAGGTGGAGGCCGGGCAGGTGGAGGCC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.296 in 151,340 control chromosomes in the GnomAD database, including 6,902 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (6902 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.295 AC: 44681 AN: 151228 Hom.: 6891 Cov.: 0

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.296 AC: 44738 AN: 151340 Hom.: 6902 Cov.: 0 AF XY: 0.291 AC XY: 21477 AN XY: 73892

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.300

Alfa AF: 0.0966 Hom.: 178

Bravo AF: 0.298

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5745946; hg19: chr1-12226785;