rs9286919

Variant names:

• chr1-178704939-A-C
• rs9286919

Your query was ambiguous. Multiple possible variants found:

• chr1-178704939-A-C
• chr1-178704939-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;