rs16902172

Variant names:

• chr8-127485797-A-G
• rs16902172

Your query was ambiguous. Multiple possible variants found:

• chr8-127485797-A-G
• chr8-127485797-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 0.173 in 152,122 control chromosomes in the GnomAD database, including 2,829 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 0.17 (2829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 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: 0.173 AC: 26368 AN: 152002 Hom.: 2832 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.173 AC: 26357 AN: 152122 Hom.: 2829 Cov.: 32 AF XY: 0.180 AC XY: 13409 AN XY: 74346

African (AFR) AF: 0.0565 AC: 2345 AN: 41538

American (AMR) AF: 0.257 AC: 3924 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1422 AN: 5182

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2704 AN: 10534

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13208 AN: 67984

Other (OTH) AF: 0.191 AC: 402 AN: 2106

Alfa AF: 0.185 Hom.: 1167

Bravo AF: 0.173

Asia WGS AF: 0.233 AC: 806 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.54
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs16902172; hg19: chr8-128498042;