rs16864968

chr2-223594965-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 0.111 in 152,238 control chromosomes in the GnomAD database, including 2,253 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 0.11 (2253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

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 = 0.313 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: 0.110 AC: 16803 AN: 152120 Hom.: 2239 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0180

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.111 AC: 16844 AN: 152238 Hom.: 2253 Cov.: 32 AF XY: 0.110 AC XY: 8210 AN XY: 74448

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0180

Gnomad4 NFE AF: 0.0205

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.0349 Hom.: 624

Bravo AF: 0.122

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16864968; hg19: chr2-224459683;