rs16892766

Variant names:

• chr8-116618444-A-C
• rs16892766

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -10 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Moderate

The variant 8-116618444-A-C has been identified. The variant allele was found at a cumulative frequency of 0.0913 (AC=13,900) in the gnomAD database across 152,184 control chromosomes, including 752 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.124. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.091 (752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.26
• Publications: 189 publications found

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -10 points.

• BP4: Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Moderate).
• BA1: GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.1241 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	0.0914	13895	751	152066	32
GnomAD4 genome	0.0913	13900	752	152184	32
TOPMed (Bravo)	0.0879	23272	1237	264690
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	0.0803	64209	2804	799766
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	0.0739	173	7	2342
ChinaMAP Phase 1	0.000886
Denmark Genome	0.111	33		296
GenomeAsia100K	0.0460	161		3476
Qatari Genome	0.190	33		174
ToMMo 61KJPN (+60KJPN MNV)	0.0000900	11	1	122252
Turkish Variome	0.0912	141	10	1546
UK10K	0.0836	632		7562
WBBC (Westlake BioBank for Chinese) pilot	0.000558	5	0	8960

Showing 13 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated prediction	Prediction	Score
AlphaGenome AVI	Uncertain	-	17
BayesDel_noAF	Benign	-	-0.39
CADD	Benign	-	22
DANN	Benign	-	0.75
GPN-Star LLR	N/A	-	-4.8
GPN-Star score	N/A	-	4.8
PhyloP100	Uncertain	-	4.3

Showing 7 of 7 scores

Other links and lift over

dbSNP: rs16892766;

hg19: chr8-117630683;

COSMIC: COSV58902220;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar