11-27731216-T-C

Variant names:

• chr11-27731216-T-C
• rs1491851
• ENST00000530663.1:n.148-34694A>G

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-34694A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,054 control chromosomes in the GnomAD database, including 14,797 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 0.41 (14797 hom., cov: 33)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 25 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255496	ENST00000530663.1	TSL:1	n.148-34694A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61768 AN: 151934 Hom.: 14794 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.406 AC: 61794 AN: 152054 Hom.: 14797 Cov.: 33 AF XY: 0.405 AC XY: 30067 AN XY: 74330

African (AFR) AF: 0.153 AC: 6367 AN: 41488

American (AMR) AF: 0.398 AC: 6078 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1468 AN: 3462

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5158

South Asian (SAS) AF: 0.397 AC: 1913 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6110 AN: 10570

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36890 AN: 67962

Other (OTH) AF: 0.412 AC: 870 AN: 2110

Alfa AF: 0.484 Hom.: 24113

Bravo AF: 0.384

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
DANN	Benign	0.63
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1491851; hg19: chr11-27752763;