chr1-67281732-A-C

Variant names:

• chr1-67281732-A-C
• rs12119179

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 0.304 in 152,122 control chromosomes in the GnomAD database, including 7,672 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 (7672 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 27 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 (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46272 AN: 152004 Hom.: 7667 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.304 AC: 46315 AN: 152122 Hom.: 7672 Cov.: 33 AF XY: 0.312 AC XY: 23176 AN XY: 74342

African (AFR) AF: 0.214 AC: 8874 AN: 41514

American (AMR) AF: 0.246 AC: 3759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1112 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2578 AN: 5184

South Asian (SAS) AF: 0.536 AC: 2585 AN: 4826

European-Finnish (FIN) AF: 0.424 AC: 4478 AN: 10558

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21919 AN: 67984

Other (OTH) AF: 0.306 AC: 643 AN: 2102

Alfa AF: 0.313 Hom.: 27349

Bravo AF: 0.283

Asia WGS AF: 0.473 AC: 1642 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	6.1
DANN	Benign	0.57
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs12119179; hg19: chr1-67747415;