XR_007086230.1:n.10666A>G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805686.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304698	ENST00000805686.1		n.610+9085A>G		intron	N/A

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 v4.9

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;