rs9409929

Variant names:

• chr9-134448667-G-A
• rs9409929
• XR_007061841.1:n.357+3108G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061841.1(LOC105376311):​n.357+3108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,100 control chromosomes in the GnomAD database, including 7,049 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 0.29 (7049 hom., cov: 33)
• Consequence: LOC105376311 XR_007061841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840

Genes affected

LOC105376311 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376311	XR_007061841.1	n.357+3108G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44717 AN: 151982 Hom.: 7041 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.294 AC: 44748 AN: 152100 Hom.: 7049 Cov.: 33 AF XY: 0.293 AC XY: 21817 AN XY: 74352

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.310

Alfa AF: 0.340 Hom.: 8070

Bravo AF: 0.280

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9409929; hg19: chr9-137340513;