rs1997325

chr2-22600878-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 0.829 in 152,160 control chromosomes in the GnomAD database, including 52,434 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 0.83 (52434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.901 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: 0.829 AC: 125998 AN: 152042 Hom.: 52387 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.829 AC: 126101 AN: 152160 Hom.: 52434 Cov.: 33 AF XY: 0.829 AC XY: 61631 AN XY: 74368

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.839

Alfa AF: 0.846 Hom.: 57789

Bravo AF: 0.817

Asia WGS AF: 0.885 AC: 3063 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.5
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1997325; hg19: chr2-22823750;