rs16904191

Variant names:

• chr8-130021250-A-G
• rs16904191

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 0.362 in 151,966 control chromosomes in the GnomAD database, including 10,510 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 0.36 (10510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 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: 0.362 AC: 55003 AN: 151848 Hom.: 10500 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.362 AC: 55055 AN: 151966 Hom.: 10510 Cov.: 32 AF XY: 0.366 AC XY: 27190 AN XY: 74278

African (AFR) AF: 0.439 AC: 18195 AN: 41448

American (AMR) AF: 0.378 AC: 5769 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3466

East Asian (EAS) AF: 0.597 AC: 3084 AN: 5170

South Asian (SAS) AF: 0.519 AC: 2502 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2478 AN: 10532

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20493 AN: 67952

Other (OTH) AF: 0.394 AC: 829 AN: 2106

Alfa AF: 0.351 Hom.: 2889

Bravo AF: 0.375

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.13
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs16904191; hg19: chr8-131033496;