rs1417999

Positions:

• chr9-101348395-A-G

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.101348395A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;