chr9-101834687-T-G

Variant names:

• chr9-101834687-T-G
• rs2786717
• XR_930187.3:n.135-11594A>C

Variant summary

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

The XR_930187.3(LOC105376187):​n.135-11594A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,054 control chromosomes in the GnomAD database, including 44,907 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 0.77 (44907 hom., cov: 32)
• Consequence: LOC105376187 XR_930187.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 0 publications found

Genes affected

LOC105376187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.766 AC: 116421 AN: 151936 Hom.: 44858 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.766 AC: 116528 AN: 152054 Hom.: 44907 Cov.: 32 AF XY: 0.761 AC XY: 56562 AN XY: 74324

African (AFR) AF: 0.838 AC: 34778 AN: 41502

American (AMR) AF: 0.774 AC: 11817 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2624 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4586 AN: 5176

South Asian (SAS) AF: 0.678 AC: 3272 AN: 4824

European-Finnish (FIN) AF: 0.634 AC: 6686 AN: 10552

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50195 AN: 67956

Other (OTH) AF: 0.777 AC: 1637 AN: 2108

Alfa AF: 0.752 Hom.: 53705

Bravo AF: 0.787

Asia WGS AF: 0.773 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2786717; hg19: chr9-104596969;