rs11065729

Variant names:

• chr12-110839684-T-C
• rs11065729
• ENST00000551161.1:n.217-5915T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000551161.1(ENSG00000257268):​n.217-5915T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,202 control chromosomes in the GnomAD database, including 8,998 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 0.28 (8998 hom., cov: 33)
• Consequence: ENSG00000257268 ENST00000551161.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.11
• Publications: 1 publications found

Genes affected

ENSG00000257268 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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
ENSG00000257268	ENST00000551161.1	n.217-5915T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42247 AN: 152084 Hom.: 8957 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.278 AC: 42338 AN: 152202 Hom.: 8998 Cov.: 33 AF XY: 0.272 AC XY: 20259 AN XY: 74420

African (AFR) AF: 0.604 AC: 25077 AN: 41488

American (AMR) AF: 0.164 AC: 2500 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3472

East Asian (EAS) AF: 0.0982 AC: 509 AN: 5184

South Asian (SAS) AF: 0.119 AC: 574 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1878 AN: 10600

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10319 AN: 68024

Other (OTH) AF: 0.244 AC: 515 AN: 2112

Alfa AF: 0.199 Hom.: 1814

Bravo AF: 0.293

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	5.9
DANN	Benign	0.85
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs11065729; hg19: chr12-111277488;