rs1921649

Positions:

• chr2-223404472-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;