rs12990970

Variant names:

• chr2-203835966-C-T
• rs12990970

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 0.379 in 151,930 control chromosomes in the GnomAD database, including 11,310 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 0.38 (11310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57591 AN: 151812 Hom.: 11313 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.379 AC: 57596 AN: 151930 Hom.: 11310 Cov.: 31 AF XY: 0.377 AC XY: 27970 AN XY: 74276

African (AFR) AF: 0.301 AC: 12462 AN: 41424

American (AMR) AF: 0.413 AC: 6307 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3464

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5160

South Asian (SAS) AF: 0.593 AC: 2858 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3257 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28261 AN: 67932

Other (OTH) AF: 0.436 AC: 918 AN: 2104

Alfa AF: 0.390 Hom.: 1486

Bravo AF: 0.378

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs12990970; hg19: chr2-204700689;