chr2-21048398-C-A

Variant names:

• chr2-21048398-C-A
• rs1713223

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 0.473 in 151,890 control chromosomes in the GnomAD database, including 18,246 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 0.47 (18246 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.473 AC: 71783 AN: 151770 Hom.: 18239 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.473 AC: 71801 AN: 151890 Hom.: 18246 Cov.: 31 AF XY: 0.481 AC XY: 35689 AN XY: 74212

African (AFR) AF: 0.290 AC: 12015 AN: 41386

American (AMR) AF: 0.504 AC: 7692 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1584 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4507 AN: 5158

South Asian (SAS) AF: 0.683 AC: 3281 AN: 4804

European-Finnish (FIN) AF: 0.573 AC: 6039 AN: 10544

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34904 AN: 67948

Other (OTH) AF: 0.510 AC: 1073 AN: 2104

Alfa AF: 0.492 Hom.: 3229

Bravo AF: 0.458

Asia WGS AF: 0.753 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1713223; hg19: chr2-21271270;