rs1921649

Variant names:

• chr2-223404472-A-G
• rs1921649

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 0.638 in 151,904 control chromosomes in the GnomAD database, including 31,768 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 0.64 (31768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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 (AFR) allele frequency at 95% confidence interval = 0.789 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: 0.638 AC: 96786 AN: 151786 Hom.: 31709 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.638 AC: 96913 AN: 151904 Hom.: 31768 Cov.: 32 AF XY: 0.639 AC XY: 47451 AN XY: 74230

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.639

Alfa AF: 0.593 Hom.: 3390

Bravo AF: 0.646

Asia WGS AF: 0.652 AC: 2263 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1921649; hg19: chr2-224269190;