rs16867225

Variant names:

• chr2-180176559-G-A
• rs16867225

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 0.134 in 151,704 control chromosomes in the GnomAD database, including 2,022 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 0.13 (2022 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 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: 0.134 AC: 20292 AN: 151588 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.134 AC: 20326 AN: 151704 Hom.: 2022 Cov.: 32 AF XY: 0.136 AC XY: 10103 AN XY: 74144

African (AFR) AF: 0.250 AC: 10356 AN: 41386

American (AMR) AF: 0.141 AC: 2145 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1615 AN: 5170

South Asian (SAS) AF: 0.189 AC: 909 AN: 4810

European-Finnish (FIN) AF: 0.0772 AC: 805 AN: 10434

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0576 AC: 3909 AN: 67916

Other (OTH) AF: 0.120 AC: 252 AN: 2108

Alfa AF: 0.0880 Hom.: 2834

Bravo AF: 0.147

Asia WGS AF: 0.260 AC: 900 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.77
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs16867225; hg19: chr2-181041286; COSMIC: COSV64706553;