1-21493549-A-G

Variant names:

• chr1-21493549-A-G
• rs12132412

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.315 in 151,908 control chromosomes in the GnomAD database, including 9,271 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 0.31 (9271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.408 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: 0.315 AC: 47845 AN: 151790 Hom.: 9271 Cov.: 31

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.315 AC: 47835 AN: 151908 Hom.: 9271 Cov.: 31 AF XY: 0.318 AC XY: 23649 AN XY: 74252

African (AFR) AF: 0.0768 AC: 3183 AN: 41458

American (AMR) AF: 0.417 AC: 6360 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1640 AN: 5152

South Asian (SAS) AF: 0.377 AC: 1813 AN: 4806

European-Finnish (FIN) AF: 0.398 AC: 4195 AN: 10534

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27856 AN: 67930

Other (OTH) AF: 0.360 AC: 758 AN: 2108

Alfa AF: 0.294 Hom.: 1637

Bravo AF: 0.302

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	5.3
DANN	Benign	0.87
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs12132412; hg19: chr1-21820042;