17-48976466-T-C

Variant names:

• chr17-48976466-T-C
• rs9899404

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 0.625 in 152,066 control chromosomes in the GnomAD database, including 30,082 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 0.62 (30082 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.624 AC: 94882 AN: 151948 Hom.: 30026 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.625 AC: 95001 AN: 152066 Hom.: 30082 Cov.: 33 AF XY: 0.624 AC XY: 46367 AN XY: 74328

African (AFR) AF: 0.722 AC: 29961 AN: 41482

American (AMR) AF: 0.636 AC: 9708 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3611 AN: 5174

South Asian (SAS) AF: 0.564 AC: 2717 AN: 4816

European-Finnish (FIN) AF: 0.569 AC: 6016 AN: 10576

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39127 AN: 67970

Other (OTH) AF: 0.600 AC: 1268 AN: 2114

Alfa AF: 0.584 Hom.: 109786

Bravo AF: 0.633

Asia WGS AF: 0.656 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.90
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs9899404; hg19: chr17-47053828;