XR_007066338.1:n.2171G>T

Variant names:

• chr18-35406636-C-A
• rs1362858
• XR_007066338.1:n.2171G>T

Variant summary

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

The XR_007066338.1(LOC105372063):​n.2171G>T 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 0.707 in 152,076 control chromosomes in the GnomAD database, including 38,069 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 0.71 (38069 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC105372063 XR_007066338.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 7 publications found

Genes affected

LOC105372063 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372063	XR_007066338.1	n.2171G>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105372063	XR_935376.3	n.402+2037G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275512	ENST00000612496.1	n.-108G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107491 AN: 151958 Hom.: 38039 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.707 AC: 107575 AN: 152076 Hom.: 38069 Cov.: 32 AF XY: 0.708 AC XY: 52633 AN XY: 74354

African (AFR) AF: 0.700 AC: 29033 AN: 41486

American (AMR) AF: 0.734 AC: 11204 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2278 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3706 AN: 5168

South Asian (SAS) AF: 0.687 AC: 3312 AN: 4822

European-Finnish (FIN) AF: 0.716 AC: 7580 AN: 10580

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.709 AC: 48199 AN: 67964

Other (OTH) AF: 0.687 AC: 1451 AN: 2112

Alfa AF: 0.708 Hom.: 140908

Bravo AF: 0.712

Asia WGS AF: 0.730 AC: 2538 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs1362858; hg19: chr18-32986600;