rs1713223

Variant names:

• chr2-21048398-C-A
• rs1713223

Your query was ambiguous. Multiple possible variants found:

• chr2-21048398-C-A
• chr2-21048398-C-G
• chr2-21048398-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.510

Alfa AF: 0.461 Hom.: 1539

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1713223; hg19: chr2-21271270;