rs16856187

Variant names:

• chr2-168913876-A-C
• rs16856187

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 0.0628 in 152,220 control chromosomes in the GnomAD database, including 634 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 0.063 (634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.0627 AC: 9532 AN: 152102 Hom.: 630 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0628 AC: 9561 AN: 152220 Hom.: 634 Cov.: 32 AF XY: 0.0677 AC XY: 5039 AN XY: 74434

African (AFR) AF: 0.110 AC: 4574 AN: 41516

American (AMR) AF: 0.0779 AC: 1191 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5170

South Asian (SAS) AF: 0.115 AC: 556 AN: 4820

European-Finnish (FIN) AF: 0.0504 AC: 535 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 960 AN: 68018

Other (OTH) AF: 0.0543 AC: 115 AN: 2116

Alfa AF: 0.0512 Hom.: 89

Bravo AF: 0.0654

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.34
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs16856187; hg19: chr2-169770386;