rs11301693

Variant names:

• chr5-109927521-CT-C
• rs11301693
• ENST00000812526.1:n.217+4515delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000812526.1(ENSG00000305706):​n.217+4515delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,184 control chromosomes in the GnomAD database, including 811 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (811 hom., cov: 32)
• Consequence: ENSG00000305706 ENST00000812526.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 0 publications found

Genes affected

ENSG00000305706 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812526.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305706	ENST00000812526.1		n.217+4515delT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9644 AN: 152068 Hom.: 806 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0636 AC: 9677 AN: 152184 Hom.: 811 Cov.: 32 AF XY: 0.0621 AC XY: 4619 AN XY: 74404

African (AFR) AF: 0.183 AC: 7591 AN: 41476

American (AMR) AF: 0.0235 AC: 360 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3470

East Asian (EAS) AF: 0.0715 AC: 370 AN: 5176

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4830

European-Finnish (FIN) AF: 0.00396 AC: 42 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0125 AC: 850 AN: 68018

Other (OTH) AF: 0.0563 AC: 119 AN: 2112

Alfa AF: 0.00336 Hom.: 1

Bravo AF: 0.0708

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs11301693; hg19: chr5-109263222;