11-27726124-G-A

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 ENST00000530663.1(ENSG00000255496):​n.148-29602C>T variant causes a intron 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: ENSG00000255496 ENST00000530663.1 intron
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902652	XR_007062633.1	n.592G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.148-29602C>T		intron_variant	Intron 1 of 1	1
ENSG00000309152	ENST00000839060.1	n.547G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000309152	ENST00000839061.1	n.558G>A		non_coding_transcript_exon_variant	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 v4.3

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;