rs1445130

Variant names:

• chr2-18653385-A-G
• rs1445130
• XR_007086230.1:n.10666A>G

Variant summary

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

The XR_007086230.1(LOC105373456):​n.10666A>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 0.116 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_007086230.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 6 publications found

Genes affected

LOC105373456 (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 (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373456	XR_007086230.1	n.10666A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105373456	XR_001739304.3	n.853+9085A>G		intron_variant	Intron 3 of 5
LOC105373456	XR_001739311.2	n.368+9085A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304698	ENST00000805686.1	n.610+9085A>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.137 AC: 5682 AN: 41492

American (AMR) AF: 0.105 AC: 1606 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3468

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5162

South Asian (SAS) AF: 0.0857 AC: 413 AN: 4820

European-Finnish (FIN) AF: 0.0713 AC: 755 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8190 AN: 67974

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.119 Hom.: 2758

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1445130; hg19: chr2-18834651;