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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986437	XR_001742825.3	n.5882T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;