rs11839053

Variant names:

• chr13-106410694-T-C
• rs11839053
• ENST00000753311.1:n.148+6874A>G

Variant summary

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

The ENST00000753311.1(ENSG00000298145):​n.148+6874A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0672 in 152,260 control chromosomes in the GnomAD database, including 445 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 0.067 (445 hom., cov: 32)
• Consequence: ENSG00000298145 ENST00000753311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 4 publications found

Genes affected

ENSG00000298145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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
ENSG00000298145	ENST00000753311.1	n.148+6874A>G		intron_variant	Intron 1 of 1
ENSG00000298164	ENST00000753443.1	n.266+2784T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0671 AC: 10204 AN: 152142 Hom.: 442 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0672 AC: 10230 AN: 152260 Hom.: 445 Cov.: 32 AF XY: 0.0664 AC XY: 4943 AN XY: 74440

African (AFR) AF: 0.126 AC: 5250 AN: 41528

American (AMR) AF: 0.0751 AC: 1148 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0209 AC: 101 AN: 4824

European-Finnish (FIN) AF: 0.0793 AC: 842 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0389 AC: 2645 AN: 68024

Other (OTH) AF: 0.0435 AC: 92 AN: 2116

Alfa AF: 0.0491 Hom.: 196

Bravo AF: 0.0707

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.056
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11839053; hg19: chr13-107063042;