9-25500240-A-G

Position:

• chr9-25500240-A-G

Variant summary

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

The XR_001746637.2(LOC107987056):​n.271-21875T>C 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 0.237 in 152,056 control chromosomes in the GnomAD database, including 4,531 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 0.24 (4531 hom., cov: 32)
• Consequence: LOC107987056 XR_001746637.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

Genes affected

LOC107987056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987056	XR_001746637.2	n.271-21875T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36011 AN: 151938 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.237 AC: 36035 AN: 152056 Hom.: 4531 Cov.: 32 AF XY: 0.240 AC XY: 17840 AN XY: 74330

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.241

Alfa AF: 0.248 Hom.: 6966

Bravo AF: 0.237

Asia WGS AF: 0.308 AC: 1073 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332173; hg19: chr9-25500238;