rs16848123

Variant names:

• chr2-163183884-A-G
• rs16848123

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 0.207 in 151,942 control chromosomes in the GnomAD database, including 3,988 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 0.21 (3988 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.208 AC: 31508 AN: 151824 Hom.: 3981 Cov.: 31

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.207 AC: 31522 AN: 151942 Hom.: 3988 Cov.: 31 AF XY: 0.211 AC XY: 15670 AN XY: 74240

African (AFR) AF: 0.0695 AC: 2884 AN: 41514

American (AMR) AF: 0.243 AC: 3699 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1970 AN: 5152

South Asian (SAS) AF: 0.168 AC: 806 AN: 4810

European-Finnish (FIN) AF: 0.309 AC: 3256 AN: 10544

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17071 AN: 67898

Other (OTH) AF: 0.251 AC: 529 AN: 2106

Alfa AF: 0.240 Hom.: 2408

Bravo AF: 0.201

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs16848123; hg19: chr2-164040394;