11-2180108-C-T

Variant names:

• chr11-2180108-C-T
• rs11564709
• ENST00000729856.1:n.177+2060C>T

Variant summary

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

The ENST00000729856.1(ENSG00000295409):​n.177+2060C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 152,220 control chromosomes in the GnomAD database, including 414 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 0.063 (414 hom., cov: 33)
• Consequence: ENSG00000295409 ENST00000729856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 6 publications found

Genes affected

ENSG00000295409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 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
ENSG00000295409	ENST00000729856.1	n.177+2060C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9530 AN: 152104 Hom.: 414 Cov.: 33

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0626 AC: 9531 AN: 152220 Hom.: 414 Cov.: 33 AF XY: 0.0617 AC XY: 4590 AN XY: 74428

African (AFR) AF: 0.0151 AC: 627 AN: 41558

American (AMR) AF: 0.0466 AC: 713 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.0541 AC: 261 AN: 4820

European-Finnish (FIN) AF: 0.0939 AC: 996 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0944 AC: 6420 AN: 67996

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0649 Hom.: 259

Bravo AF: 0.0564

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.67
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs11564709; hg19: chr11-2201338; COSMIC: COSV51398906;