17-48985115-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0764

Gnomad4 AMR AF: 0.0786

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0750

Gnomad4 NFE AF: 0.0305

Gnomad4 OTH AF: 0.0649

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.70
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9894411; hg19: chr17-47062477;