rs1713223

Positions:

• chr2-21048398-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;