chr2-210804282-T-C

Variant names:

• chr2-210804282-T-C
• rs12998006

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 0.236 in 151,912 control chromosomes in the GnomAD database, including 4,691 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 0.24 (4691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.276 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: 0.236 AC: 35899 AN: 151794 Hom.: 4689 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.236 AC: 35906 AN: 151912 Hom.: 4691 Cov.: 32 AF XY: 0.239 AC XY: 17769 AN XY: 74242

African (AFR) AF: 0.130 AC: 5397 AN: 41480

American (AMR) AF: 0.278 AC: 4233 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3466

East Asian (EAS) AF: 0.153 AC: 791 AN: 5166

South Asian (SAS) AF: 0.245 AC: 1178 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3797 AN: 10566

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18964 AN: 67896

Other (OTH) AF: 0.209 AC: 440 AN: 2106

Alfa AF: 0.264 Hom.: 1252

Bravo AF: 0.226

Asia WGS AF: 0.185 AC: 646 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	3.4
DANN	Benign	0.75
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs12998006; hg19: chr2-211669006;