11-73183228-C-T

Variant names:

• chr11-73183228-C-T
• rs11603160
• ENST00000759218.1:n.-24C>T

Variant summary

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

The ENST00000759218.1(ENSG00000298945):​n.-24C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,178 control chromosomes in the GnomAD database, including 1,584 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 0.13 (1584 hom., cov: 32)
• Consequence: ENSG00000298945 ENST00000759218.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 12 publications found

Genes affected

ENSG00000298945 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759218.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298945	ENST00000759218.1		n.-24C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19595 AN: 152060 Hom.: 1582 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.129 AC: 19595 AN: 152178 Hom.: 1584 Cov.: 32 AF XY: 0.125 AC XY: 9288 AN XY: 74396

African (AFR) AF: 0.0510 AC: 2117 AN: 41544

American (AMR) AF: 0.157 AC: 2400 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3468

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5174

South Asian (SAS) AF: 0.0893 AC: 431 AN: 4824

European-Finnish (FIN) AF: 0.113 AC: 1191 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11894 AN: 67992

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.157 Hom.: 5000

Bravo AF: 0.133

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.61
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs11603160; hg19: chr11-72894273;