rs16864968

Variant names:

• chr2-223594965-A-G
• rs16864968

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.318 AC: 13179 AN: 41496

American (AMR) AF: 0.0576 AC: 881 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5178

South Asian (SAS) AF: 0.0419 AC: 202 AN: 4826

European-Finnish (FIN) AF: 0.0180 AC: 191 AN: 10620

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0205 AC: 1394 AN: 68020

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0489 Hom.: 2841

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs16864968; hg19: chr2-224459683;