17-48531741-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 0.47 in 152,060 control chromosomes in the GnomAD database, including 17,431 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 0.47 (17431 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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: 0.470 AC: 71458 AN: 151942 Hom.: 17415 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.470 AC: 71499 AN: 152060 Hom.: 17431 Cov.: 31 AF XY: 0.471 AC XY: 34977 AN XY: 74332

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.510

Alfa AF: 0.516 Hom.: 22955

Bravo AF: 0.466

Asia WGS AF: 0.468 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	15
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11079828; hg19: chr17-46609103;