chr17-54891767-T-G

Variant names:

• chr17-54891767-T-G
• rs16955329

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 0.388 in 152,094 control chromosomes in the GnomAD database, including 12,406 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 0.39 (12406 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

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

GnomAD3 genomes AF: 0.388 AC: 59034 AN: 151976 Hom.: 12396 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.388 AC: 59086 AN: 152094 Hom.: 12406 Cov.: 33 AF XY: 0.389 AC XY: 28900 AN XY: 74344

African (AFR) AF: 0.544 AC: 22567 AN: 41458

American (AMR) AF: 0.407 AC: 6226 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2207 AN: 5166

South Asian (SAS) AF: 0.273 AC: 1317 AN: 4828

European-Finnish (FIN) AF: 0.346 AC: 3656 AN: 10576

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20440 AN: 67988

Other (OTH) AF: 0.395 AC: 834 AN: 2110

Alfa AF: 0.334 Hom.: 26928

Bravo AF: 0.405

Asia WGS AF: 0.394 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	10
DANN	Benign	0.88
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs16955329; hg19: chr17-52969128;