rs9457840

Variant names:

• chr6-160120316-T-C
• rs9457840
• XR_007059842.1:n.854+526A>G

Variant summary

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

The XR_007059842.1(LOC124901452):​n.854+526A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0494 in 152,280 control chromosomes in the GnomAD database, including 334 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 0.049 (334 hom., cov: 33)
• Consequence: LOC124901452 XR_007059842.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 11 publications found

Genes affected

LOC124901452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0494 AC: 7513 AN: 152162 Hom.: 333 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.00800

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0494 AC: 7524 AN: 152280 Hom.: 334 Cov.: 33 AF XY: 0.0508 AC XY: 3784 AN XY: 74476

African (AFR) AF: 0.110 AC: 4585 AN: 41546

American (AMR) AF: 0.0418 AC: 640 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.127 AC: 655 AN: 5172

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4820

European-Finnish (FIN) AF: 0.00800 AC: 85 AN: 10628

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1055 AN: 68024

Other (OTH) AF: 0.0331 AC: 70 AN: 2116

Alfa AF: 0.0285 Hom.: 159

Bravo AF: 0.0532

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.46
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9457840; hg19: chr6-160541348;