17-48976466-T-C

Position:

• chr17-48976466-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 0.625 in 152,066 control chromosomes in the GnomAD database, including 30,082 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 0.62 (30082 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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: 0.624 AC: 94882 AN: 151948 Hom.: 30026 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.625 AC: 95001 AN: 152066 Hom.: 30082 Cov.: 33 AF XY: 0.624 AC XY: 46367 AN XY: 74328

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.600

Alfa AF: 0.574 Hom.: 50959

Bravo AF: 0.633

Asia WGS AF: 0.656 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9899404; hg19: chr17-47053828;