11-2179933-T-C

Variant names:

• chr11-2179933-T-C
• rs6578993
• ENST00000729856.1:n.177+1885T>C

Variant summary

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

The ENST00000729856.1(ENSG00000295409):​n.177+1885T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,110 control chromosomes in the GnomAD database, including 55,119 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 0.85 (55119 hom., cov: 31)
• Consequence: ENSG00000295409 ENST00000729856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 10 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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+1885T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129127 AN: 151992 Hom.: 55068 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.850 AC: 129239 AN: 152110 Hom.: 55119 Cov.: 31 AF XY: 0.848 AC XY: 63023 AN XY: 74348

African (AFR) AF: 0.916 AC: 38006 AN: 41504

American (AMR) AF: 0.752 AC: 11495 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3024 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4490 AN: 5146

South Asian (SAS) AF: 0.830 AC: 4000 AN: 4818

European-Finnish (FIN) AF: 0.834 AC: 8838 AN: 10592

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56651 AN: 67980

Other (OTH) AF: 0.851 AC: 1801 AN: 2116

Alfa AF: 0.837 Hom.: 67925

Bravo AF: 0.849

Asia WGS AF: 0.854 AC: 2972 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	2.3
DANN	Benign	0.42
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6578993; hg19: chr11-2201163;