rs1360286

Positions:

• chr9-21293632-C-A

Variant summary

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

The XR_001746634.2(LOC107987053):​n.471+24676C>A 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 0.248 in 151,692 control chromosomes in the GnomAD database, including 4,933 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 0.25 (4933 hom., cov: 30)
• Consequence: LOC107987053 XR_001746634.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

LOC107987053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987053	XR_001746634.2	n.471+24676C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37620 AN: 151572 Hom.: 4925 Cov.: 30

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.248 AC: 37675 AN: 151692 Hom.: 4933 Cov.: 30 AF XY: 0.248 AC XY: 18408 AN XY: 74104

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.245

Alfa AF: 0.223 Hom.: 2897

Bravo AF: 0.260

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1360286; hg19: chr9-21293631;