rs13354021

Variant names:

• chr5-100943585-T-C
• rs13354021
• XR_001742825.3:n.5882T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-100943585-T-C
• chr5-100943585-T-G

Variant summary

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

The XR_001742825.3(LOC107986437):​n.5882T>C 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 0.366 in 151,946 control chromosomes in the GnomAD database, including 10,363 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 0.37 (10363 hom., cov: 32)
• Consequence: LOC107986437 XR_001742825.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 8 publications found

Genes affected

LOC107986437 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.366 AC: 55519 AN: 151828 Hom.: 10356 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.366 AC: 55538 AN: 151946 Hom.: 10363 Cov.: 32 AF XY: 0.366 AC XY: 27219 AN XY: 74276

African (AFR) AF: 0.347 AC: 14389 AN: 41428

American (AMR) AF: 0.316 AC: 4824 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3464

East Asian (EAS) AF: 0.248 AC: 1286 AN: 5176

South Asian (SAS) AF: 0.295 AC: 1424 AN: 4822

European-Finnish (FIN) AF: 0.425 AC: 4491 AN: 10560

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26792 AN: 67916

Other (OTH) AF: 0.357 AC: 753 AN: 2112

Alfa AF: 0.383 Hom.: 6930

Bravo AF: 0.358

Asia WGS AF: 0.270 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs13354021; hg19: chr5-100279289; COSMIC: COSV60170828;