XR_007058205.1:n.59A>G

Variant names:

• chr4-102621044-T-C
• rs10489113
• XR_007058205.1:n.59A>G

Variant summary

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

The XR_007058205.1(LOC105377347):​n.59A>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 0.252 in 152,086 control chromosomes in the GnomAD database, including 6,077 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 0.25 (6077 hom., cov: 32)
• Consequence: LOC105377347 XR_007058205.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 23 publications found

Genes affected

LOC105377347 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377347	XR_007058205.1	n.59A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304360	ENST00000802886.1	n.-213A>G		upstream_gene_variant
ENSG00000304360	ENST00000802887.1	n.-212A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38234 AN: 151968 Hom.: 6069 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.252 AC: 38264 AN: 152086 Hom.: 6077 Cov.: 32 AF XY: 0.246 AC XY: 18317 AN XY: 74384

African (AFR) AF: 0.443 AC: 18343 AN: 41444

American (AMR) AF: 0.180 AC: 2745 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3468

East Asian (EAS) AF: 0.0843 AC: 436 AN: 5174

South Asian (SAS) AF: 0.185 AC: 894 AN: 4820

European-Finnish (FIN) AF: 0.0966 AC: 1026 AN: 10616

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13153 AN: 67984

Other (OTH) AF: 0.260 AC: 548 AN: 2104

Alfa AF: 0.218 Hom.: 12096

Bravo AF: 0.264

Asia WGS AF: 0.139 AC: 482 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	6.8
DANN	Benign	0.67
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10489113; hg19: chr4-103542201;