15-45339670-A-G

Variant names:

• chr15-45339670-A-G
• rs1153862
• XR_007064609.1:n.195-2419A>G

Variant summary

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

The XR_007064609.1(LOC124903482):​n.195-2419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,926 control chromosomes in the GnomAD database, including 27,369 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 0.56 (27369 hom., cov: 31)
• Consequence: LOC124903482 XR_007064609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932
• Publications: 10 publications found

Genes affected

LOC124903482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.561 AC: 85091 AN: 151808 Hom.: 27313 Cov.: 31

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.561 AC: 85211 AN: 151926 Hom.: 27369 Cov.: 31 AF XY: 0.568 AC XY: 42144 AN XY: 74254

African (AFR) AF: 0.843 AC: 34925 AN: 41448

American (AMR) AF: 0.620 AC: 9465 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4669 AN: 5176

South Asian (SAS) AF: 0.593 AC: 2860 AN: 4822

European-Finnish (FIN) AF: 0.411 AC: 4327 AN: 10526

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.376 AC: 25549 AN: 67916

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.492 Hom.: 13298

Bravo AF: 0.592

Asia WGS AF: 0.735 AC: 2553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1153862; hg19: chr15-45631868;