11-18050016-T-G

Variant names:

• chr11-18050016-T-G
• rs7110238
• ENST00000787024.1:n.97-15032T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000787024.1(ENSG00000302464):​n.97-15032T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,804 control chromosomes in the GnomAD database, including 18,207 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 0.47 (18207 hom., cov: 30)
• Consequence: ENSG00000302464 ENST00000787024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

Genes affected

ENSG00000302464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787024.1. 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
	ENSG00000302464	ENST00000787024.1		n.97-15032T>G		intron	N/A
	ENSG00000302464	ENST00000787025.1		n.98-11922T>G		intron	N/A
	ENSG00000302464	ENST00000787026.1		n.94-11922T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71286 AN: 151684 Hom.: 18159 Cov.: 30

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.470 AC: 71390 AN: 151804 Hom.: 18207 Cov.: 30 AF XY: 0.461 AC XY: 34221 AN XY: 74156

African (AFR) AF: 0.670 AC: 27706 AN: 41382

American (AMR) AF: 0.368 AC: 5611 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1155 AN: 5140

South Asian (SAS) AF: 0.341 AC: 1635 AN: 4798

European-Finnish (FIN) AF: 0.385 AC: 4060 AN: 10534

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28632 AN: 67910

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.400 Hom.: 4481

Bravo AF: 0.479

Asia WGS AF: 0.321 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.66
PhyloP100		-1.4

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: rs7110238;

hg19: chr11-18071563;