chr17-48976466-T-C

Variant names:

• chr17-48976466-T-C
• rs9899404

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;