chr2-201104217-G-A

Variant names:

• chr2-201104217-G-A
• rs12621441

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 0.133 in 152,048 control chromosomes in the GnomAD database, including 1,592 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 0.13 (1592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20233 AN: 151930 Hom.: 1594 Cov.: 32

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.133 AC: 20221 AN: 152048 Hom.: 1592 Cov.: 32 AF XY: 0.133 AC XY: 9894 AN XY: 74318

African (AFR) AF: 0.0346 AC: 1436 AN: 41476

American (AMR) AF: 0.165 AC: 2514 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3472

East Asian (EAS) AF: 0.185 AC: 957 AN: 5172

South Asian (SAS) AF: 0.127 AC: 612 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1869 AN: 10562

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11686 AN: 67980

Other (OTH) AF: 0.133 AC: 280 AN: 2108

Alfa AF: 0.145 Hom.: 2307

Bravo AF: 0.127

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.8
DANN	Benign	0.82
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12621441; hg19: chr2-201968940;