chr1-209807412-G-A

Variant names:

• chr1-209807412-G-A
• rs1005287

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 0.375 in 151,922 control chromosomes in the GnomAD database, including 11,090 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 (11090 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 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: 0.375 AC: 56934 AN: 151804 Hom.: 11090 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.375 AC: 56950 AN: 151922 Hom.: 11090 Cov.: 31 AF XY: 0.380 AC XY: 28200 AN XY: 74260

African (AFR) AF: 0.280 AC: 11590 AN: 41412

American (AMR) AF: 0.502 AC: 7655 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1018 AN: 3472

East Asian (EAS) AF: 0.567 AC: 2921 AN: 5154

South Asian (SAS) AF: 0.439 AC: 2114 AN: 4812

European-Finnish (FIN) AF: 0.401 AC: 4234 AN: 10550

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26186 AN: 67944

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.368 Hom.: 1283

Bravo AF: 0.379

Asia WGS AF: 0.427 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.31
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs1005287; hg19: chr1-209980757;