11-27724217-C-T

Variant names:

• chr11-27724217-C-T
• rs908867
• ENST00000530663.1:n.148-27695G>A

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-27695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,106 control chromosomes in the GnomAD database, including 743 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 0.091 (743 hom., cov: 33)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 53 publications found

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902652	XR_007062633.1	n.246-1561C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.148-27695G>A		intron_variant	Intron 1 of 1	1
ENSG00000309152	ENST00000839060.1	n.201-1561C>T		intron_variant	Intron 2 of 2
ENSG00000309152	ENST00000839061.1	n.212-1561C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0909 AC: 13819 AN: 151988 Hom.: 738 Cov.: 33

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0910 AC: 13846 AN: 152106 Hom.: 743 Cov.: 33 AF XY: 0.0945 AC XY: 7028 AN XY: 74374

African (AFR) AF: 0.0822 AC: 3409 AN: 41470

American (AMR) AF: 0.0607 AC: 927 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3466

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5174

South Asian (SAS) AF: 0.252 AC: 1212 AN: 4816

European-Finnish (FIN) AF: 0.116 AC: 1230 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0945 AC: 6426 AN: 67992

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.0865 Hom.: 1196

Bravo AF: 0.0826

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.16
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs908867; hg19: chr11-27745764;