9-25500240-A-G

Variant names:

• chr9-25500240-A-G
• rs1332173
• XR_001746637.2:n.271-21875T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746637.2(LOC107987056):​n.271-21875T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 3 publications found

Genes affected

LOC107987056 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.164 AC: 6794 AN: 41498

American (AMR) AF: 0.288 AC: 4395 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3468

East Asian (EAS) AF: 0.387 AC: 1988 AN: 5140

South Asian (SAS) AF: 0.312 AC: 1502 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2576 AN: 10572

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17155 AN: 67980

Other (OTH) AF: 0.241 AC: 509 AN: 2110

Alfa AF: 0.247 Hom.: 9536

Bravo AF: 0.237

Asia WGS AF: 0.308 AC: 1073 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1332173; hg19: chr9-25500238;