rs16848123

chr2-163183884-A-G

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 0.207 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.251

Alfa AF: 0.236 Hom.: 1432

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16848123; hg19: chr2-164040394;