ENST00000530663.1:n.148-30216C>T

Variant names:

• chr11-27726738-G-A
• rs11030123
• ENST00000530663.1:n.148-30216C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000530663.1(ENSG00000255496):​n.148-30216C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,192 control chromosomes in the GnomAD database, including 745 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 0.091 (745 hom., cov: 32)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902652	XR_007062633.1	n.1206G>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.148-30216C>T		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.0909 AC: 13822 AN: 152074 Hom.: 740 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.0910 AC: 13849 AN: 152192 Hom.: 745 Cov.: 32 AF XY: 0.0944 AC XY: 7023 AN XY: 74422

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0347

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0924 Hom.: 155

Bravo AF: 0.0826

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11030123; hg19: chr11-27748285;