11-27723312-T-C

Position:

• chr11-27723312-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902652	XR_007062633.1	n.245+826T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.148-26790A>G		intron_variant		1

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

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.0954

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.168

Alfa AF: 0.175 Hom.: 3248

Bravo AF: 0.151

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12273363; hg19: chr11-27744859;