9-1463618-A-G

Variant names:

• chr9-1463618-A-G
• rs10124818
• XR_002956872.2:n.357-525A>G

Variant summary

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

The XR_929415.3(LOC102723803):​n.357-525A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,010 control chromosomes in the GnomAD database, including 14,401 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 0.35 (14401 hom., cov: 31)
• Consequence: LOC102723803 XR_929415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 6 publications found

Genes affected

LOC102723803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.352 AC: 53528 AN: 151892 Hom.: 14363 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.353 AC: 53612 AN: 152010 Hom.: 14401 Cov.: 31 AF XY: 0.346 AC XY: 25679 AN XY: 74316

African (AFR) AF: 0.762 AC: 31574 AN: 41424

American (AMR) AF: 0.254 AC: 3882 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.132 AC: 680 AN: 5164

South Asian (SAS) AF: 0.178 AC: 858 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1986 AN: 10590

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12852 AN: 67962

Other (OTH) AF: 0.303 AC: 640 AN: 2110

Alfa AF: 0.245 Hom.: 17986

Bravo AF: 0.376

Asia WGS AF: 0.185 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.48
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10124818; hg19: chr9-1463618;