11-131322488-A-G

Variant names:

• chr11-131322488-A-G
• rs1793783
• ENST00000606885.1:n.147-27821A>G

Variant summary

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

The ENST00000606885.1(ENSG00000231698):​n.147-27821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,260 control chromosomes in the GnomAD database, including 1,278 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 0.11 (1278 hom., cov: 32)
• Consequence: ENSG00000231698 ENST00000606885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 2 publications found

Genes affected

ENSG00000231698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606885.1. 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
	ENSG00000231698	ENST00000606885.1	TSL:1	n.147-27821A>G		intron	N/A
	ENSG00000231698	ENST00000834706.1		n.185-27821A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16968 AN: 152142 Hom.: 1279 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.111 AC: 16961 AN: 152260 Hom.: 1278 Cov.: 32 AF XY: 0.108 AC XY: 8026 AN XY: 74430

African (AFR) AF: 0.0302 AC: 1256 AN: 41554

American (AMR) AF: 0.106 AC: 1619 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3472

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5176

South Asian (SAS) AF: 0.0808 AC: 390 AN: 4828

European-Finnish (FIN) AF: 0.115 AC: 1222 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11415 AN: 68012

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.114 Hom.: 432

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.4
DANN	Benign	0.89
PhyloP100		0.32

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: rs1793783;

hg19: chr11-131192383;