9-32290483-T-C

Position:

• chr9-32290483-T-C

Variant summary

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

The XR_001746645.2(LOC107987059):​n.488-7978A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,190 control chromosomes in the GnomAD database, including 1,319 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 0.12 (1319 hom., cov: 32)
• Consequence: LOC107987059 XR_001746645.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

LOC107987059 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987059	XR_001746645.2	n.488-7978A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18033 AN: 152072 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0906

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.119 AC: 18056 AN: 152190 Hom.: 1319 Cov.: 32 AF XY: 0.119 AC XY: 8843 AN XY: 74414

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0154

Gnomad4 NFE AF: 0.0906

Gnomad4 OTH AF: 0.149

Alfa AF: 0.107 Hom.: 186

Bravo AF: 0.134

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7873766; hg19: chr9-32290481;