rs13129209

Variant names:

• chr4-180155034-T-C
• rs13129209
• ENST00000826655.1:n.194+6100T>C

Variant summary

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

The ENST00000826655.1(ENSG00000307510):​n.194+6100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,086 control chromosomes in the GnomAD database, including 25,056 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 0.53 (25056 hom., cov: 33)
• Consequence: ENSG00000307510 ENST00000826655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 5 publications found

Genes affected

ENSG00000307510 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 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
ENSG00000307510	ENST00000826655.1	n.194+6100T>C		intron_variant	Intron 2 of 2
ENSG00000307510	ENST00000826656.1	n.229+5253T>C		intron_variant	Intron 3 of 3
ENSG00000307510	ENST00000826657.1	n.153+6100T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80589 AN: 151968 Hom.: 25058 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.530 AC: 80598 AN: 152086 Hom.: 25056 Cov.: 33 AF XY: 0.537 AC XY: 39887 AN XY: 74334

African (AFR) AF: 0.187 AC: 7771 AN: 41488

American (AMR) AF: 0.549 AC: 8375 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2034 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3657 AN: 5140

South Asian (SAS) AF: 0.632 AC: 3047 AN: 4822

European-Finnish (FIN) AF: 0.730 AC: 7725 AN: 10588

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.680 AC: 46223 AN: 68004

Other (OTH) AF: 0.547 AC: 1158 AN: 2116

Alfa AF: 0.621 Hom.: 82174

Bravo AF: 0.503

Asia WGS AF: 0.600 AC: 2088 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	7.9
DANN	Benign	0.71
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs13129209; hg19: chr4-181076187;