rs16865545

Variant names:

• chr2-224082453-A-G
• rs16865545

Your query was ambiguous. Multiple possible variants found:

• chr2-224082453-A-G
• chr2-224082453-A-T

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 0.135 in 152,272 control chromosomes in the GnomAD database, including 1,593 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 (1593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.135 AC: 20536 AN: 152154 Hom.: 1592 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20531 AN: 152272 Hom.: 1593 Cov.: 32 AF XY: 0.135 AC XY: 10066 AN XY: 74448

African (AFR) AF: 0.0579 AC: 2409 AN: 41584

American (AMR) AF: 0.153 AC: 2346 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.145 AC: 751 AN: 5186

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1361 AN: 10606

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

European-Non Finnish (NFE) AF: 0.166 AC: 11308 AN: 68002

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.144 Hom.: 214

Bravo AF: 0.133

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.79
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs16865545; hg19: chr2-224947170;