XR_007061478.1:n.4375+1854C>G

Variant names:

• chr9-37368456-C-G
• rs308516
• XR_007061478.1:n.4375+1854C>G

Variant summary

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

The XR_007061478.1(LOC124902153):​n.4375+1854C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 149,572 control chromosomes in the GnomAD database, including 174 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 0.032 (174 hom., cov: 31)
• Consequence: LOC124902153 XR_007061478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 1 publications found

Genes affected

LOC124902153 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 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: 0.0316 AC: 4723 AN: 149458 Hom.: 173 Cov.: 31

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.00555

Gnomad MID AF: 0.0329

Gnomad NFE AF: 0.00316

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0316 AC: 4732 AN: 149572 Hom.: 174 Cov.: 31 AF XY: 0.0333 AC XY: 2426 AN XY: 72834

African (AFR) AF: 0.0801 AC: 3242 AN: 40492

American (AMR) AF: 0.0186 AC: 278 AN: 14940

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3462

East Asian (EAS) AF: 0.0744 AC: 376 AN: 5052

South Asian (SAS) AF: 0.0722 AC: 341 AN: 4724

European-Finnish (FIN) AF: 0.00555 AC: 55 AN: 9916

Middle Eastern (MID) AF: 0.0355 AC: 10 AN: 282

European-Non Finnish (NFE) AF: 0.00316 AC: 214 AN: 67718

Other (OTH) AF: 0.0303 AC: 63 AN: 2076

Alfa AF: 0.00494 Hom.: 2

Bravo AF: 0.0329

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs308516; hg19: chr9-37368453;