11-27723312-T-C

Variant names:

• chr11-27723312-T-C
• rs12273363
• ENST00000530663.1:n.148-26790A>G

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-26790A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,258 control chromosomes in the GnomAD database, including 2,150 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 (2150 hom., cov: 33)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 67 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=-0.38).
• 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: 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.148-26790A>G		intron	N/A
	ENSG00000309152	ENST00000839060.1		n.200+826T>C		intron	N/A
	ENSG00000309152	ENST00000839061.1		n.211+826T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23881 AN: 152140 Hom.: 2151 Cov.: 33

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.157 AC: 23887 AN: 152258 Hom.: 2150 Cov.: 33 AF XY: 0.155 AC XY: 11563 AN XY: 74452

African (AFR) AF: 0.0926 AC: 3849 AN: 41572

American (AMR) AF: 0.167 AC: 2549 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3472

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5176

South Asian (SAS) AF: 0.0954 AC: 460 AN: 4822

European-Finnish (FIN) AF: 0.248 AC: 2628 AN: 10600

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13338 AN: 67996

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.175 Hom.: 4136

Bravo AF: 0.151

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	18
DANN	Benign	0.76
PhyloP100		2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12273363;

hg19: chr11-27744859;