13-110773496-G-A

Variant names:

• chr13-110773496-G-A
• rs2083567
• XR_001750022.2:n.2153G>A

Variant summary

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

The XR_001750022.2(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_001750022.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

Genes affected

LOC107984613 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107984613	XR_001750022.2	n.2153G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC107984613	XR_001750023.2	n.2153G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC107984613	XR_001750024.2	n.2153G>A		non_coding_transcript_exon_variant	Exon 1 of 4
LOC107984613	XR_007063873.1	n.2153G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.206 AC: 8534 AN: 41512

American (AMR) AF: 0.421 AC: 6431 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3472

East Asian (EAS) AF: 0.429 AC: 2222 AN: 5178

South Asian (SAS) AF: 0.576 AC: 2776 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3938 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31198 AN: 67982

Other (OTH) AF: 0.422 AC: 888 AN: 2104

Alfa AF: 0.438 Hom.: 11144

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2083567; hg19: chr13-111425843;