3-117508453-T-G

Position:

• chr3-117508453-T-G

Variant summary

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

The XR_924361.3(LOC105374056):​n.25133T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,098 control chromosomes in the GnomAD database, including 1,627 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 0.13 (1627 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374056	XR_007096021.1	n.25133T>G		non_coding_transcript_exon_variant	1/3
LOC105374056	XR_924361.3	n.25133T>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19810 AN: 151980 Hom.: 1627 Cov.: 32

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.130 AC: 19807 AN: 152098 Hom.: 1627 Cov.: 32 AF XY: 0.127 AC XY: 9455 AN XY: 74322

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0522

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0894 Hom.: 131

Bravo AF: 0.123

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45530132; hg19: chr3-117227300;