rs2922126

chr3-172449471-T-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 0.28 in 151,948 control chromosomes in the GnomAD database, including 6,959 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 0.28 (6959 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.280 AC: 42468 AN: 151828 Hom.: 6954 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.280 AC: 42480 AN: 151948 Hom.: 6959 Cov.: 31 AF XY: 0.286 AC XY: 21228 AN XY: 74274

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.309

Alfa AF: 0.303 Hom.: 939

Bravo AF: 0.261

Asia WGS AF: 0.440 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.57
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: rs2922126; hg19: chr3-172167261;