rs2083567

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-110773496-G-A
• chr13-110773496-G-C
• chr13-110773496-G-T

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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 v4.9

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;