chr11-27728178-T-C

Variant names:

• chr11-27728178-T-C
• rs1491850
• ENST00000530663.1:n.148-31656A>G

Variant summary

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

The XR_007062633.1(LOC124902652):​n.2646T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,106 control chromosomes in the GnomAD database, including 11,090 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 0.37 (11090 hom., cov: 33)
• Consequence: LOC124902652 XR_007062633.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• Publications: 61 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530663.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255496	ENST00000530663.1	TSL:1	n.148-31656A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56811 AN: 151988 Hom.: 11081 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.374 AC: 56850 AN: 152106 Hom.: 11090 Cov.: 33 AF XY: 0.373 AC XY: 27723 AN XY: 74356

African (AFR) AF: 0.265 AC: 10994 AN: 41478

American (AMR) AF: 0.369 AC: 5639 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3466

East Asian (EAS) AF: 0.466 AC: 2415 AN: 5178

South Asian (SAS) AF: 0.390 AC: 1876 AN: 4810

European-Finnish (FIN) AF: 0.426 AC: 4503 AN: 10580

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28616 AN: 67978

Other (OTH) AF: 0.386 AC: 815 AN: 2114

Alfa AF: 0.406 Hom.: 40960

Bravo AF: 0.369

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.7
DANN	Benign	0.32
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1491850; hg19: chr11-27749725;