rs13134869

Variant names:

• chr4-143782301-A-G
• rs13134869
• ENST00000499587.2:n.179-26013A>G

Variant summary

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

The ENST00000499587.2(ENSG00000251600):​n.179-26013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,120 control chromosomes in the GnomAD database, including 5,961 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 0.26 (5961 hom., cov: 32)
• Consequence: ENSG00000251600 ENST00000499587.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

ENSG00000251600 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251600	ENST00000499587.2	n.179-26013A>G		intron_variant	Intron 2 of 6	4
ENSG00000251600	ENST00000641328.1	n.1004+43184A>G		intron_variant	Intron 3 of 6
ENSG00000251600	ENST00000641556.1	n.250+43184A>G		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40237 AN: 152002 Hom.: 5957 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.265 AC: 40257 AN: 152120 Hom.: 5961 Cov.: 32 AF XY: 0.266 AC XY: 19794 AN XY: 74362

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.285

Alfa AF: 0.293 Hom.: 851

Bravo AF: 0.257

Asia WGS AF: 0.205 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13134869; hg19: chr4-144703454;