rs16867225

chr2-180176559-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 0.134 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0743 Hom.: 1311

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

Splicing

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

Publications

LitVar

Other links and lift over

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