9-101834687-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376187	XR_930187.3	n.135-11594A>C		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;