rs13188771

Variant names:

• chr5-101612841-C-A
• rs13188771
• XR_001742829.2:n.201+18293G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-101612841-C-A
• chr5-101612841-C-G

Variant summary

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

The XR_948628.3(LOC105379102):​n.464+18293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,180 control chromosomes in the GnomAD database, including 1,783 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 0.14 (1783 hom., cov: 31)
• Consequence: LOC105379102 XR_948628.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

Genes affected

LOC105379102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379102	XR_001742829.2	n.201+18293G>T		intron_variant	Intron 2 of 4
LOC105379102	XR_007058891.1	n.464+18293G>T		intron_variant	Intron 4 of 5
LOC105379102	XR_948628.3	n.464+18293G>T		intron_variant	Intron 4 of 6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20545 AN: 152062 Hom.: 1770 Cov.: 31

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.135 AC: 20571 AN: 152180 Hom.: 1783 Cov.: 31 AF XY: 0.137 AC XY: 10174 AN XY: 74400

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.172

Alfa AF: 0.158 Hom.: 3561

Bravo AF: 0.140

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13188771; hg19: chr5-100948545;