17-48486345-G-T

Variant names:

• chr17-48486345-G-T
• rs1553754

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 0.495 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
• Publications: 6 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 = 0.721 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.290 AC: 12016 AN: 41430

American (AMR) AF: 0.570 AC: 8712 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1986 AN: 3468

East Asian (EAS) AF: 0.741 AC: 3834 AN: 5176

South Asian (SAS) AF: 0.511 AC: 2459 AN: 4812

European-Finnish (FIN) AF: 0.575 AC: 6035 AN: 10488

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38427 AN: 67936

Other (OTH) AF: 0.543 AC: 1148 AN: 2114

Alfa AF: 0.531 Hom.: 9194

Bravo AF: 0.488

Asia WGS AF: 0.557 AC: 1940 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	0.21
DANN	Benign	0.56
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1553754; hg19: chr17-46563707;