17-43745857-T-G

Variant names:

• chr17-43745857-T-G
• rs9899889

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.525 in 152,144 control chromosomes in the GnomAD database, including 22,254 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 0.53 (22254 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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: 0.525 AC: 79763 AN: 152026 Hom.: 22192 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.525 AC: 79883 AN: 152144 Hom.: 22254 Cov.: 33 AF XY: 0.527 AC XY: 39212 AN XY: 74374

African (AFR) AF: 0.722 AC: 29970 AN: 41492

American (AMR) AF: 0.478 AC: 7306 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2156 AN: 5174

South Asian (SAS) AF: 0.480 AC: 2315 AN: 4822

European-Finnish (FIN) AF: 0.551 AC: 5837 AN: 10584

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29565 AN: 67996

Other (OTH) AF: 0.469 AC: 990 AN: 2112

Alfa AF: 0.444 Hom.: 9023

Bravo AF: 0.527

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs9899889; hg19: chr17-41823225;