17-48873613-C-T

Position:

• chr17-48873613-C-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 0.114 in 152,094 control chromosomes in the GnomAD database, including 1,775 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 0.11 (1775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

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 (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.113 AC: 17235 AN: 151976 Hom.: 1760 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.114 AC: 17290 AN: 152094 Hom.: 1775 Cov.: 32 AF XY: 0.114 AC XY: 8495 AN XY: 74372

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.0529

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0641

Gnomad4 NFE AF: 0.0414

Gnomad4 OTH AF: 0.0797

Alfa AF: 0.0395 Hom.: 61

Bravo AF: 0.118

Asia WGS AF: 0.134 AC: 467 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	0.92
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8079874; hg19: chr17-46950975;