9-1911291-G-T

Variant names:

• chr9-1911291-G-T
• rs10811102
• XR_001746599.1:n.143-50830G>T

Variant summary

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

The XR_001746599.1(LOC105375951):​n.143-50830G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,902 control chromosomes in the GnomAD database, including 5,433 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 0.23 (5433 hom., cov: 31)
• Consequence: LOC105375951 XR_001746599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 5 publications found

Genes affected

LOC105375951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 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: 0.231 AC: 34994 AN: 151784 Hom.: 5409 Cov.: 31

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.231 AC: 35027 AN: 151902 Hom.: 5433 Cov.: 31 AF XY: 0.237 AC XY: 17575 AN XY: 74234

African (AFR) AF: 0.0724 AC: 3002 AN: 41454

American (AMR) AF: 0.378 AC: 5769 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3488 AN: 5158

South Asian (SAS) AF: 0.310 AC: 1497 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2074 AN: 10512

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17474 AN: 67910

Other (OTH) AF: 0.287 AC: 605 AN: 2110

Alfa AF: 0.251 Hom.: 6301

Bravo AF: 0.239

Asia WGS AF: 0.485 AC: 1687 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.35
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10811102; hg19: chr9-1911291;