rs13183130

chr5-3609839-T-C

Variant summary

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

The XR_001742554.2(LOC107986399):n.4280T>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 0.0412 in 152,262 control chromosomes in the GnomAD database, including 187 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 0.041 (187 hom., cov: 33)
• Consequence: LOC107986399 XR_001742554.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

Genes affected

LOC107986399 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.062 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986399	XR_001742554.2	n.4280T>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0412 AC: 6275 AN: 152144 Hom.: 188 Cov.: 33

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0310

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

GnomAD4 genome AF: 0.0412 AC: 6275 AN: 152262 Hom.: 187 Cov.: 33 AF XY: 0.0400 AC XY: 2980 AN XY: 74462

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0303

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0636

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0542 Hom.: 125

Bravo AF: 0.0350

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13183130; hg19: chr5-3609953;