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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901452	XR_007059842.1	n.854+526A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;