rs12288512

Variant names:

• chr11-27726124-G-A
• rs12288512
• ENST00000530663.1:n.148-29602C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000839060.1(ENSG00000309152):​n.547G>A 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 0.156 in 152,076 control chromosomes in the GnomAD database, including 2,130 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 0.16 (2130 hom., cov: 32)
• Consequence: ENSG00000309152 ENST00000839060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 10 publications found

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839060.1. 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.148-29602C>T		intron	N/A
	ENSG00000309152	ENST00000839060.1		n.547G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000309152	ENST00000839061.1		n.558G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23757 AN: 151958 Hom.: 2131 Cov.: 32

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.156 AC: 23763 AN: 152076 Hom.: 2130 Cov.: 32 AF XY: 0.155 AC XY: 11494 AN XY: 74324

African (AFR) AF: 0.0915 AC: 3799 AN: 41524

American (AMR) AF: 0.165 AC: 2527 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3466

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5186

South Asian (SAS) AF: 0.0957 AC: 461 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2626 AN: 10548

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13292 AN: 67954

Other (OTH) AF: 0.167 AC: 351 AN: 2108

Alfa AF: 0.169 Hom.: 402

Bravo AF: 0.150

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs12288512; hg19: chr11-27747671;