rs1445130

Positions:

• chr2-18653385-A-G

Variant summary

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

The XR_007086234.1(LOC105373456):​n.853+9085A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,090 control chromosomes in the GnomAD database, including 1,106 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 0.12 (1106 hom., cov: 32)
• Consequence: LOC105373456 XR_007086234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

Genes affected

LOC105373456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373456	XR_007086234.1	n.853+9085A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17579 AN: 151972 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.116 AC: 17600 AN: 152090 Hom.: 1106 Cov.: 32 AF XY: 0.113 AC XY: 8436 AN XY: 74370

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0269

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.120

Alfa AF: 0.120 Hom.: 1054

Bravo AF: 0.120

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
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: rs1445130; hg19: chr2-18834651;