rs16896091

Variant names:

• chr5-26785742-T-C
• rs16896091

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 0.341 in 151,434 control chromosomes in the GnomAD database, including 9,686 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 0.34 (9686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51580 AN: 151316 Hom.: 9673 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.341 AC: 51611 AN: 151434 Hom.: 9686 Cov.: 32 AF XY: 0.336 AC XY: 24822 AN XY: 73974

African (AFR) AF: 0.505 AC: 20791 AN: 41210

American (AMR) AF: 0.304 AC: 4633 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1378 AN: 3458

East Asian (EAS) AF: 0.165 AC: 851 AN: 5144

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2237 AN: 10510

Middle Eastern (MID) AF: 0.345 AC: 100 AN: 290

European-Non Finnish (NFE) AF: 0.284 AC: 19236 AN: 67776

Other (OTH) AF: 0.350 AC: 738 AN: 2108

Alfa AF: 0.306 Hom.: 27930

Bravo AF: 0.355

Asia WGS AF: 0.215 AC: 747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.68
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs16896091; hg19: chr5-26785851; COSMIC: COSV70154403;