9-108074792-A-G

Variant names:

• chr9-108074792-A-G
• rs10816625
• XR_001746881.2:n.721-21498T>C

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-21498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 152,324 control chromosomes in the GnomAD database, including 837 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 0.071 (837 hom., cov: 33)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• Publications: 27 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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: 0.0709 AC: 10797 AN: 152206 Hom.: 833 Cov.: 33

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.0709 AC: 10799 AN: 152324 Hom.: 837 Cov.: 33 AF XY: 0.0737 AC XY: 5493 AN XY: 74486

African (AFR) AF: 0.0170 AC: 708 AN: 41588

American (AMR) AF: 0.131 AC: 2007 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2099 AN: 5170

South Asian (SAS) AF: 0.0793 AC: 383 AN: 4830

European-Finnish (FIN) AF: 0.0647 AC: 687 AN: 10616

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4371 AN: 68030

Other (OTH) AF: 0.0978 AC: 207 AN: 2116

Alfa AF: 0.0724 Hom.: 2125

Bravo AF: 0.0803

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10816625; hg19: chr9-110837073;