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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375951	XR_001746599.1	n.143-50830G>T		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;