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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.257 AC: 10611 AN: 41352

American (AMR) AF: 0.437 AC: 6674 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3466

East Asian (EAS) AF: 0.356 AC: 1841 AN: 5178

South Asian (SAS) AF: 0.394 AC: 1897 AN: 4810

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10550

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27867 AN: 67970

Other (OTH) AF: 0.381 AC: 806 AN: 2114

Alfa AF: 0.394 Hom.: 20369

Bravo AF: 0.364

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs9286919; hg19: chr1-178674074;