17-48985115-T-C

Variant names:

• chr17-48985115-T-C
• rs9894411

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 0.0699 in 152,098 control chromosomes in the GnomAD database, including 941 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 0.070 (941 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10579 AN: 151980 Hom.: 928 Cov.: 31

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0305

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0699 AC: 10628 AN: 152098 Hom.: 941 Cov.: 31 AF XY: 0.0754 AC XY: 5607 AN XY: 74354

African (AFR) AF: 0.0764 AC: 3170 AN: 41488

American (AMR) AF: 0.0786 AC: 1199 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2487 AN: 5164

South Asian (SAS) AF: 0.127 AC: 609 AN: 4808

European-Finnish (FIN) AF: 0.0750 AC: 795 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0305 AC: 2071 AN: 67994

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0440 Hom.: 38

Bravo AF: 0.0710

Asia WGS AF: 0.291 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs9894411; hg19: chr17-47062477;