rs1417999

Variant names:

• chr9-101348395-A-G
• rs1417999

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 0.448 in 152,082 control chromosomes in the GnomAD database, including 18,148 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 0.45 (18148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 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: 0.448 AC: 68148 AN: 151964 Hom.: 18148 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.448 AC: 68145 AN: 152082 Hom.: 18148 Cov.: 33 AF XY: 0.441 AC XY: 32762 AN XY: 74328

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.494

Alfa AF: 0.585 Hom.: 40157

Bravo AF: 0.427

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.97
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417999; hg19: chr9-104110677;