rs11108839

Variant names:

• chr12-97141104-A-G
• rs11108839
• ENST00000716365.1:n.206-44085A>G

Variant summary

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

The ENST00000716365.1(ENSG00000257470):​n.206-44085A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,160 control chromosomes in the GnomAD database, including 1,770 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 0.13 (1770 hom., cov: 32)
• Consequence: ENSG00000257470 ENST00000716365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 3 publications found

Genes affected

ENSG00000257470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716365.1. 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
	ENSG00000257470	ENST00000716365.1		n.206-44085A>G		intron	N/A
	ENSG00000257470	ENST00000716366.1		n.185-43972A>G		intron	N/A
	ENSG00000257470	ENST00000716367.1		n.55-43972A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19653 AN: 152042 Hom.: 1758 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.129 AC: 19702 AN: 152160 Hom.: 1770 Cov.: 32 AF XY: 0.131 AC XY: 9750 AN XY: 74400

African (AFR) AF: 0.241 AC: 9985 AN: 41474

American (AMR) AF: 0.179 AC: 2743 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 315 AN: 3472

East Asian (EAS) AF: 0.127 AC: 656 AN: 5172

South Asian (SAS) AF: 0.125 AC: 602 AN: 4818

European-Finnish (FIN) AF: 0.0752 AC: 797 AN: 10596

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.0625 AC: 4252 AN: 68020

Other (OTH) AF: 0.128 AC: 270 AN: 2112

Alfa AF: 0.110 Hom.: 538

Bravo AF: 0.145

Asia WGS AF: 0.133 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.8
DANN	Benign	0.73
PhyloP100		0.0020
Mutation Taster		=100/0	polymorphism

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: rs11108839;

hg19: chr12-97534882;