17-48486345-G-T

Position:

• chr17-48486345-G-T

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 0.495 in 151,898 control chromosomes in the GnomAD database, including 19,808 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 0.50 (19808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669

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 = 0.721 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: 0.495 AC: 75170 AN: 151788 Hom.: 19800 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.495 AC: 75191 AN: 151898 Hom.: 19808 Cov.: 32 AF XY: 0.497 AC XY: 36883 AN XY: 74210

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.543

Alfa AF: 0.500 Hom.: 4275

Bravo AF: 0.488

Asia WGS AF: 0.557 AC: 1940 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	0.21
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553754; hg19: chr17-46563707;