XR_001746881.2:n.720+18137G>T

Variant names:

• chr9-108292529-C-A
• rs1570504
• XR_001746881.2:n.720+18137G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746881.2(LOC105376214):​n.720+18137G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,984 control chromosomes in the GnomAD database, including 4,803 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 0.22 (4803 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.720+18137G>T		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.720+18137G>T		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.720+18137G>T		intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33438 AN: 151866 Hom.: 4792 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.220 AC: 33474 AN: 151984 Hom.: 4803 Cov.: 32 AF XY: 0.220 AC XY: 16344 AN XY: 74286

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.192

Alfa AF: 0.147 Hom.: 2467

Bravo AF: 0.223

Asia WGS AF: 0.108 AC: 376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1570504; hg19: chr9-111054809;