rs2083567

chr13-110773496-G-A

Variant summary

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

The XR_007063873.1(LOC107984613):n.2153G>A 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 0.381 in 152,118 control chromosomes in the GnomAD database, including 12,035 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 0.38 (12035 hom., cov: 33)
• Consequence: LOC107984613 XR_007063873.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

LOC107984613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984613	XR_007063873.1	n.2153G>A		non_coding_transcript_exon_variant	1/2
LOC107984613	XR_001750022.2	n.2153G>A		non_coding_transcript_exon_variant	1/3
LOC107984613	XR_001750023.2	n.2153G>A		non_coding_transcript_exon_variant	1/3
LOC107984613	XR_001750024.2	n.2153G>A		non_coding_transcript_exon_variant	1/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57965 AN: 152000 Hom.: 12032 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.381 AC: 57987 AN: 152118 Hom.: 12035 Cov.: 33 AF XY: 0.382 AC XY: 28432 AN XY: 74356

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.422

Alfa AF: 0.439 Hom.: 8033

Bravo AF: 0.375

Asia WGS AF: 0.449 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.50
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2083567; hg19: chr13-111425843;