rs9286919

chr1-178704939-A-Cchr1-178704939-A-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 0.366 in 151,912 control chromosomes in the GnomAD database, including 10,641 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 0.37 (10641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.428 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: 0.366 AC: 55591 AN: 151792 Hom.: 10630 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.366 AC: 55622 AN: 151912 Hom.: 10641 Cov.: 32 AF XY: 0.364 AC XY: 26992 AN XY: 74250

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.381

Alfa AF: 0.397 Hom.: 16217

Bravo AF: 0.364

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.8
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9286919; hg19: chr1-178674074;