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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903482	XR_007064609.1	n.195-2419A>G		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;