rs921322

chr2-11179534-G-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 0.396 in 151,940 control chromosomes in the GnomAD database, including 13,412 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 0.40 (13412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.505 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: 0.396 AC: 60061 AN: 151822 Hom.: 13398 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.396 AC: 60095 AN: 151940 Hom.: 13412 Cov.: 32 AF XY: 0.395 AC XY: 29313 AN XY: 74236

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.416

Alfa AF: 0.480 Hom.: 23760

Bravo AF: 0.392

Asia WGS AF: 0.424 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921322; hg19: chr2-11319660;